diff --git a/ApplicationCode/Application/RiaApplication.cpp b/ApplicationCode/Application/RiaApplication.cpp
index 923fa9b9df..382d54894c 100644
--- a/ApplicationCode/Application/RiaApplication.cpp
+++ b/ApplicationCode/Application/RiaApplication.cpp
@@ -335,7 +335,7 @@ bool RiaApplication::loadProject(const QString& projectFileName, ProjectLoadActi
     m_project->fileName = projectFileName;
     m_project->readFile();
 
-    // Apply any modifiactions to the loaded project before we go ahead and load actual data
+    // Apply any modifications to the loaded project before we go ahead and load actual data
     if (projectModifier)
     {
         projectModifier->applyModificationsToProject(m_project);
@@ -366,6 +366,25 @@ bool RiaApplication::loadProject(const QString& projectFileName, ProjectLoadActi
         return true;
     }
 
+    if (m_project->show3DWindow())
+    {
+        RiuMainWindow::instance()->show();
+    }
+    else
+    {
+        RiuMainWindow::instance()->close();
+    }
+
+    if (m_project->showPlotWindow())
+    {
+        RiaApplication::instance()->getOrCreateAndShowMainPlotWindow();
+    }
+    else if (mainPlotWindow())
+    {
+        mainPlotWindow()->close();
+    }
+
+
     ///////
     // Load the external data, and initialize stuff that needs specific ordering
     
diff --git a/ApplicationCode/CMakeLists.txt b/ApplicationCode/CMakeLists.txt
index 22cec10d69..7941040dfd 100644
--- a/ApplicationCode/CMakeLists.txt
+++ b/ApplicationCode/CMakeLists.txt
@@ -159,6 +159,7 @@ list( APPEND REFERENCED_CMAKE_FILES
     Commands/WellPathCommands/CMakeLists_files.cmake
     Commands/CrossSectionCommands/CMakeLists_files.cmake
     Commands/IntersectionBoxCommands/CMakeLists_files.cmake
+    Commands/ApplicationCommands/CMakeLists_files.cmake
 )
 
 option (RESINSIGHT_INCLUDE_APPLICATION_UNIT_TESTS "Include ApplicationCode Unit Tests" OFF)
diff --git a/ApplicationCode/Commands/ApplicationCommands/CMakeLists_files.cmake b/ApplicationCode/Commands/ApplicationCommands/CMakeLists_files.cmake
new file mode 100644
index 0000000000..1425a44164
--- /dev/null
+++ b/ApplicationCode/Commands/ApplicationCommands/CMakeLists_files.cmake
@@ -0,0 +1,37 @@
+
+# Use this workaround until we're on 2.8.3 on all platforms and can use CMAKE_CURRENT_LIST_DIR directly 
+if (${CMAKE_VERSION} VERSION_GREATER "2.8.2")
+    set(CEE_CURRENT_LIST_DIR  ${CMAKE_CURRENT_LIST_DIR}/)
+endif()
+
+set (SOURCE_GROUP_HEADER_FILES
+${CEE_CURRENT_LIST_DIR}RicLaunchUnitTestsFeature.h
+${CEE_CURRENT_LIST_DIR}RicShowPlotWindowFeature.h
+${CEE_CURRENT_LIST_DIR}RicShowMainWindowFeature.h
+${CEE_CURRENT_LIST_DIR}RicTileWindowsFeature.h
+${CEE_CURRENT_LIST_DIR}RicTilePlotWindowsFeature.h
+)
+
+set (SOURCE_GROUP_SOURCE_FILES
+${CEE_CURRENT_LIST_DIR}RicLaunchUnitTestsFeature.cpp
+${CEE_CURRENT_LIST_DIR}RicShowPlotWindowFeature.cpp
+${CEE_CURRENT_LIST_DIR}RicShowMainWindowFeature.cpp
+${CEE_CURRENT_LIST_DIR}RicTileWindowsFeature.cpp
+${CEE_CURRENT_LIST_DIR}RicTilePlotWindowsFeature.cpp
+)
+
+list(APPEND CODE_HEADER_FILES
+${SOURCE_GROUP_HEADER_FILES}
+)
+
+list(APPEND CODE_SOURCE_FILES
+${SOURCE_GROUP_SOURCE_FILES}
+)
+
+#set (QT_MOC_HEADERS
+#${QT_MOC_HEADERS}
+#${CEE_CURRENT_LIST_DIR}RicBoxManipulatorEventHandler.h
+#)
+
+
+source_group( "CommandFeature\\Application" FILES ${SOURCE_GROUP_HEADER_FILES} ${SOURCE_GROUP_SOURCE_FILES} ${CEE_CURRENT_LIST_DIR}CMakeLists_files.cmake )
diff --git a/ApplicationCode/Commands/RicLaunchUnitTestsFeature.cpp b/ApplicationCode/Commands/ApplicationCommands/RicLaunchUnitTestsFeature.cpp
similarity index 100%
rename from ApplicationCode/Commands/RicLaunchUnitTestsFeature.cpp
rename to ApplicationCode/Commands/ApplicationCommands/RicLaunchUnitTestsFeature.cpp
diff --git a/ApplicationCode/Commands/RicLaunchUnitTestsFeature.h b/ApplicationCode/Commands/ApplicationCommands/RicLaunchUnitTestsFeature.h
similarity index 100%
rename from ApplicationCode/Commands/RicLaunchUnitTestsFeature.h
rename to ApplicationCode/Commands/ApplicationCommands/RicLaunchUnitTestsFeature.h
diff --git a/ApplicationCode/Commands/RicShowMainWindowFeature.cpp b/ApplicationCode/Commands/ApplicationCommands/RicShowMainWindowFeature.cpp
similarity index 100%
rename from ApplicationCode/Commands/RicShowMainWindowFeature.cpp
rename to ApplicationCode/Commands/ApplicationCommands/RicShowMainWindowFeature.cpp
diff --git a/ApplicationCode/Commands/RicShowMainWindowFeature.h b/ApplicationCode/Commands/ApplicationCommands/RicShowMainWindowFeature.h
similarity index 100%
rename from ApplicationCode/Commands/RicShowMainWindowFeature.h
rename to ApplicationCode/Commands/ApplicationCommands/RicShowMainWindowFeature.h
diff --git a/ApplicationCode/Commands/RicShowPlotWindowFeature.cpp b/ApplicationCode/Commands/ApplicationCommands/RicShowPlotWindowFeature.cpp
similarity index 100%
rename from ApplicationCode/Commands/RicShowPlotWindowFeature.cpp
rename to ApplicationCode/Commands/ApplicationCommands/RicShowPlotWindowFeature.cpp
diff --git a/ApplicationCode/Commands/RicShowPlotWindowFeature.h b/ApplicationCode/Commands/ApplicationCommands/RicShowPlotWindowFeature.h
similarity index 100%
rename from ApplicationCode/Commands/RicShowPlotWindowFeature.h
rename to ApplicationCode/Commands/ApplicationCommands/RicShowPlotWindowFeature.h
diff --git a/ApplicationCode/Commands/RicTilePlotWindowsFeature.cpp b/ApplicationCode/Commands/ApplicationCommands/RicTilePlotWindowsFeature.cpp
similarity index 100%
rename from ApplicationCode/Commands/RicTilePlotWindowsFeature.cpp
rename to ApplicationCode/Commands/ApplicationCommands/RicTilePlotWindowsFeature.cpp
diff --git a/ApplicationCode/Commands/RicTilePlotWindowsFeature.h b/ApplicationCode/Commands/ApplicationCommands/RicTilePlotWindowsFeature.h
similarity index 100%
rename from ApplicationCode/Commands/RicTilePlotWindowsFeature.h
rename to ApplicationCode/Commands/ApplicationCommands/RicTilePlotWindowsFeature.h
diff --git a/ApplicationCode/Commands/RicTileWindowsFeature.cpp b/ApplicationCode/Commands/ApplicationCommands/RicTileWindowsFeature.cpp
similarity index 100%
rename from ApplicationCode/Commands/RicTileWindowsFeature.cpp
rename to ApplicationCode/Commands/ApplicationCommands/RicTileWindowsFeature.cpp
diff --git a/ApplicationCode/Commands/RicTileWindowsFeature.h b/ApplicationCode/Commands/ApplicationCommands/RicTileWindowsFeature.h
similarity index 100%
rename from ApplicationCode/Commands/RicTileWindowsFeature.h
rename to ApplicationCode/Commands/ApplicationCommands/RicTileWindowsFeature.h
diff --git a/ApplicationCode/Commands/CMakeLists_files.cmake b/ApplicationCode/Commands/CMakeLists_files.cmake
index e56577193e..4f947095b5 100644
--- a/ApplicationCode/Commands/CMakeLists_files.cmake
+++ b/ApplicationCode/Commands/CMakeLists_files.cmake
@@ -45,11 +45,6 @@ ${CEE_CURRENT_LIST_DIR}RicComputeStatisticsFeature.h
 ${CEE_CURRENT_LIST_DIR}RicWellLogsImportFileFeature.h
 
 ${CEE_CURRENT_LIST_DIR}RicTogglePerspectiveViewFeature.h
-${CEE_CURRENT_LIST_DIR}RicTileWindowsFeature.h
-${CEE_CURRENT_LIST_DIR}RicTilePlotWindowsFeature.h
-${CEE_CURRENT_LIST_DIR}RicShowPlotWindowFeature.h
-${CEE_CURRENT_LIST_DIR}RicShowMainWindowFeature.h
-${CEE_CURRENT_LIST_DIR}RicLaunchUnitTestsFeature.h
 ${CEE_CURRENT_LIST_DIR}RicExportToLasFileFeature.h
 ${CEE_CURRENT_LIST_DIR}RicExportToLasFileResampleUi.h
 ${CEE_CURRENT_LIST_DIR}RicImportInputEclipseCaseOpmFeature.h
@@ -102,11 +97,6 @@ ${CEE_CURRENT_LIST_DIR}RicNewStatisticsCaseFeature.cpp
 ${CEE_CURRENT_LIST_DIR}RicComputeStatisticsFeature.cpp
 
 ${CEE_CURRENT_LIST_DIR}RicTogglePerspectiveViewFeature.cpp
-${CEE_CURRENT_LIST_DIR}RicTileWindowsFeature.cpp
-${CEE_CURRENT_LIST_DIR}RicTilePlotWindowsFeature.cpp
-${CEE_CURRENT_LIST_DIR}RicShowPlotWindowFeature.cpp
-${CEE_CURRENT_LIST_DIR}RicShowMainWindowFeature.cpp
-${CEE_CURRENT_LIST_DIR}RicLaunchUnitTestsFeature.cpp
 ${CEE_CURRENT_LIST_DIR}RicExportToLasFileFeature.cpp
 ${CEE_CURRENT_LIST_DIR}RicExportToLasFileResampleUi.cpp
 ${CEE_CURRENT_LIST_DIR}RicImportInputEclipseCaseOpmFeature.cpp
diff --git a/ApplicationCode/ProjectDataModel/RimProject.cpp b/ApplicationCode/ProjectDataModel/RimProject.cpp
index a24a52f84d..db4a184c19 100644
--- a/ApplicationCode/ProjectDataModel/RimProject.cpp
+++ b/ApplicationCode/ProjectDataModel/RimProject.cpp
@@ -48,6 +48,7 @@
 #include "RimWellPathImport.h"
 
 #include "RiuMainWindow.h"
+#include "RiuMainPlotWindow.h"
 
 #include "OctaveScriptCommands/RicExecuteScriptForCasesFeature.h"
 
@@ -102,6 +103,12 @@ RimProject::RimProject(void)
     CAF_PDM_InitFieldNoDefault(&currentModelIndexPath, "TreeViewCurrentModelIndexPath", "",  "", "", "");
     currentModelIndexPath.uiCapability()->setUiHidden(true);
 
+    CAF_PDM_InitField(&m_show3DWindow, "show3DWindow", true, "Show 3D Window", "", "", "");
+    m_show3DWindow.uiCapability()->setUiHidden(true);
+
+    CAF_PDM_InitField(&m_showPlotWindow, "showPlotWindow", false, "Show Plot Window", "", "", "");
+    m_showPlotWindow.uiCapability()->setUiHidden(true);
+
     // Obsolete fields. The content is moved to OilFields and friends
     CAF_PDM_InitFieldNoDefault(&casesObsolete, "Reservoirs", "",  "", "", "");
     casesObsolete.uiCapability()->setUiHidden(true);
@@ -324,6 +331,18 @@ void RimProject::initAfterRead()
 //--------------------------------------------------------------------------------------------------
 void RimProject::setupBeforeSave()
 {
+    m_show3DWindow = RiuMainWindow::instance()->isVisible();
+
+    if (RiaApplication::instance()->mainPlotWindow() &&
+        RiaApplication::instance()->mainPlotWindow()->isVisible())
+    {
+        m_showPlotWindow = true;
+    }
+    else
+    {
+        m_showPlotWindow = false;
+    }
+
     m_projectFileVersionString = STRPRODUCTVER;
 }
 
@@ -706,6 +725,22 @@ void RimProject::actionsBasedOnSelection(QMenu& contextMenu)
     }
 }
 
+//--------------------------------------------------------------------------------------------------
+/// 
+//--------------------------------------------------------------------------------------------------
+bool RimProject::show3DWindow() const
+{
+    return m_show3DWindow;
+}
+
+//--------------------------------------------------------------------------------------------------
+/// 
+//--------------------------------------------------------------------------------------------------
+bool RimProject::showPlotWindow() const
+{
+    return m_showPlotWindow;
+}
+
 //--------------------------------------------------------------------------------------------------
 /// 
 //--------------------------------------------------------------------------------------------------
diff --git a/ApplicationCode/ProjectDataModel/RimProject.h b/ApplicationCode/ProjectDataModel/RimProject.h
index 3c020a9a21..9fcdc6d4a6 100644
--- a/ApplicationCode/ProjectDataModel/RimProject.h
+++ b/ApplicationCode/ProjectDataModel/RimProject.h
@@ -95,6 +95,9 @@ public:
 
     void            actionsBasedOnSelection(QMenu& contextMenu);
 
+    bool            show3DWindow() const;
+    bool            showPlotWindow() const;
+
 protected:
     // Overridden methods
     void            initScriptDirectories();
@@ -107,11 +110,14 @@ private:
     void            appendScriptItems(QMenu* menu, RimScriptCollection* scriptCollection);
 
 private:
-    caf::PdmField<QString>      m_projectFileVersionString;
+    caf::PdmField<QString>  m_projectFileVersionString;
+
+    caf::PdmField<bool>     m_show3DWindow;
+    caf::PdmField<bool>     m_showPlotWindow;
 
     caf::PdmField<int>                                  nextValidCaseId;          // Unique case ID within a project, used to identify a case from Octave scripts
     caf::PdmField<int>                                  nextValidCaseGroupId;     // Unique case group ID within a project, used to identify a case group from Octave scripts
 
-    caf::PdmChildArrayField<RimEclipseCase*>                     casesObsolete; // obsolete
-    caf::PdmChildArrayField<RimIdenticalGridCaseGroup*>   caseGroupsObsolete; // obsolete
+    caf::PdmChildArrayField<RimEclipseCase*>            casesObsolete; // obsolete
+    caf::PdmChildArrayField<RimIdenticalGridCaseGroup*> caseGroupsObsolete; // obsolete
 };