diff --git a/BlueBerry/Bundles/org.blueberry.core.expressions/CMakeLists.txt b/BlueBerry/Bundles/org.blueberry.core.expressions/CMakeLists.txt
index d96a425db9..9c6ed4592a 100644
--- a/BlueBerry/Bundles/org.blueberry.core.expressions/CMakeLists.txt
+++ b/BlueBerry/Bundles/org.blueberry.core.expressions/CMakeLists.txt
@@ -1,4 +1,4 @@
 project(org_blueberry_core_expressions)
 
 MACRO_CREATE_CTK_PLUGIN(EXPORT_DIRECTIVE BERRY_EXPRESSIONS
-                        EXPORTED_INCLUDE_SUFFIXES src src/common)
+                        EXPORTED_INCLUDE_SUFFIXES src)
diff --git a/BlueBerry/Bundles/org.blueberry.ui/CMakeLists.txt b/BlueBerry/Bundles/org.blueberry.ui/CMakeLists.txt
index 99825e877d..1a06997513 100644
--- a/BlueBerry/Bundles/org.blueberry.ui/CMakeLists.txt
+++ b/BlueBerry/Bundles/org.blueberry.ui/CMakeLists.txt
@@ -1,19 +1,18 @@
 project(org_blueberry_ui)
 
 set(PLUGIN_exported_include_suffixes
   src
   src/application
-  src/commands
   src/dialogs
   src/guitk
   src/handlers
   src/intro
   src/presentations
   src/services
   src/testing
   src/tweaklets
   src/util
 )
 
 MACRO_CREATE_CTK_PLUGIN(EXPORT_DIRECTIVE BERRY_UI
                         EXPORTED_INCLUDE_SUFFIXES ${PLUGIN_exported_include_suffixes})
diff --git a/Modules/QtWidgetsExt/CMakeLists.txt b/Modules/QtWidgetsExt/CMakeLists.txt
index 7916170c25..fb35dcde93 100644
--- a/Modules/QtWidgetsExt/CMakeLists.txt
+++ b/Modules/QtWidgetsExt/CMakeLists.txt
@@ -1,6 +1,6 @@
 MITK_CREATE_MODULE(
-  INCLUDE_DIRS QmitkApplicationBase QmitkPropertyObservers QmitkFunctionalityComponents
+  INCLUDE_DIRS QmitkApplicationBase QmitkPropertyObservers
   DEPENDS MitkImageStatistics MitkQtWidgets
   PACKAGE_DEPENDS Qt4|QtWebKit Qwt Qxt
   WARNINGS_AS_ERRORS
 )
diff --git a/Modules/SceneSerialization/CMakeLists.txt b/Modules/SceneSerialization/CMakeLists.txt
index 461ad17ea5..56710c481d 100644
--- a/Modules/SceneSerialization/CMakeLists.txt
+++ b/Modules/SceneSerialization/CMakeLists.txt
@@ -1,8 +1,8 @@
 MITK_CREATE_MODULE(
-  INCLUDE_DIRS BaseDataSerializer BasePropertySerializer BasePropertyDeserializer
+  INCLUDE_DIRS BaseDataSerializer
   DEPENDS MitkSceneSerializationBase
   PACKAGE_DEPENDS Poco
   WARNINGS_AS_ERRORS
 )
 
 add_subdirectory(Testing)
diff --git a/Modules/SceneSerializationBase/CMakeLists.txt b/Modules/SceneSerializationBase/CMakeLists.txt
index 7d5f63c169..c1517fa523 100644
--- a/Modules/SceneSerializationBase/CMakeLists.txt
+++ b/Modules/SceneSerializationBase/CMakeLists.txt
@@ -1,7 +1,7 @@
 MITK_CREATE_MODULE(
-  INCLUDE_DIRS BaseDataSerializer BasePropertySerializer
+  INCLUDE_DIRS BasePropertySerializer
   DEPENDS MitkCore
   WARNINGS_AS_ERRORS
 )
 add_subdirectory(Testing)
 
diff --git a/Modules/Segmentation/CMakeLists.txt b/Modules/Segmentation/CMakeLists.txt
index fef70bd1b5..5a35144363 100644
--- a/Modules/Segmentation/CMakeLists.txt
+++ b/Modules/Segmentation/CMakeLists.txt
@@ -1,7 +1,7 @@
 MITK_CREATE_MODULE(
-  INCLUDE_DIRS Algorithms Controllers DataManagement Interactions IO Rendering SegmentationUtilities/BooleanOperations SegmentationUtilities/MorphologicalOperations
+  INCLUDE_DIRS Algorithms Controllers DataManagement Interactions Rendering SegmentationUtilities/BooleanOperations SegmentationUtilities/MorphologicalOperations
   DEPENDS MitkAlgorithmsExt MitkIpSegmentation MitkIpFunc MitkLegacyAdaptors MitkSurfaceInterpolation MitkGraphAlgorithms MitkContourModel
   PACKAGE_DEPENDS ITK|ITKBinaryMathematicalMorphology+ITKLabelVoting+ITKRegionGrowing+ITKFastMarching+ITKAnisotropicSmoothing+ITKWatersheds
 )
 
 add_subdirectory(Testing)