diff --git a/Doc/doxy.config.in b/Doc/doxy.config.in
index 4b92922f..29d93264 100644
--- a/Doc/doxy.config.in
+++ b/Doc/doxy.config.in
@@ -598,8 +598,8 @@ RECURSIVE              = YES
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
 EXCLUDE                = @CMAKE_CURRENT_SOURCE_DIR@/Examples \
-                         @CMAKE_CURRENT_SOURCE_DIR@/../Tools/Test \
-                         @CMAKE_CURRENT_SOURCE_DIR@/../Apps
+                         @CMAKE_CURRENT_SOURCE_DIR@/../src/OpenMesh/Tools/Test \
+                         @CMAKE_CURRENT_SOURCE_DIR@/../src/OpenMesh/Apps/Unsupported
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
diff --git a/src/OpenMesh/Apps/QtViewer/QGLViewerWidget.cc b/src/OpenMesh/Apps/QtViewer/QGLViewerWidget.cc
index ffde3545..9c153f23 100644
--- a/src/OpenMesh/Apps/QtViewer/QGLViewerWidget.cc
+++ b/src/OpenMesh/Apps/QtViewer/QGLViewerWidget.cc
@@ -503,7 +503,7 @@ void QGLViewerWidget::keyPressEvent( QKeyEvent* _event)
 
 
 void
-QGLViewerWidget::translate( const Vec3f& _trans )
+QGLViewerWidget::translate( const OpenMesh::Vec3f& _trans )
 {
   // Translate the object by _trans
   // Update modelview_matrix_
@@ -519,7 +519,7 @@ QGLViewerWidget::translate( const Vec3f& _trans )
 
 
 void
-QGLViewerWidget::rotate( const Vec3f& _axis, float _angle )
+QGLViewerWidget::rotate( const OpenMesh::Vec3f& _axis, float _angle )
 {
   // Rotate around center center_, axis _axis, by angle _angle
   // Update modelview_matrix_
@@ -551,7 +551,7 @@ QGLViewerWidget::rotate( const Vec3f& _axis, float _angle )
 
 
 bool
-QGLViewerWidget::map_to_sphere( const QPoint& _v2D, Vec3f& _v3D )
+QGLViewerWidget::map_to_sphere( const QPoint& _v2D, OpenMesh::Vec3f& _v3D )
 {
     // This is actually doing the Sphere/Hyperbolic sheet hybrid thing,
     // based on Ken Shoemake's ArcBall in Graphics Gems IV, 1993.
@@ -616,7 +616,7 @@ QGLViewerWidget::view_all()
 
 
 void
-QGLViewerWidget::set_scene_pos( const Vec3f& _cog, float _radius )
+QGLViewerWidget::set_scene_pos( const OpenMesh::Vec3f& _cog, float _radius )
 {
   center_ = _cog;
   radius_ = _radius;
diff --git a/src/OpenMesh/Apps/Unsupported/Streaming-qt4/Client/QGLViewerWidget.cc b/src/OpenMesh/Apps/Unsupported/Streaming-qt4/Client/QGLViewerWidget.cc
index 3222dfc0..0c2a5f43 100644
--- a/src/OpenMesh/Apps/Unsupported/Streaming-qt4/Client/QGLViewerWidget.cc
+++ b/src/OpenMesh/Apps/Unsupported/Streaming-qt4/Client/QGLViewerWidget.cc
@@ -430,7 +430,7 @@ void QGLViewerWidget::keyPressEvent( QKeyEvent* _event)
 
 
 void
-QGLViewerWidget::translate( const Vec3f& _trans )
+QGLViewerWidget::translate( const OpenMesh::Vec3f& _trans )
 {
   // Translate the object by _trans
   // Update modelview_matrix_
@@ -446,7 +446,7 @@ QGLViewerWidget::translate( const Vec3f& _trans )
 
 
 void
-QGLViewerWidget::rotate( const Vec3f& _axis, float _angle )
+QGLViewerWidget::rotate( const OpenMesh::Vec3f& _axis, float _angle )
 {
   // Rotate around center center_, axis _axis, by angle _angle
   // Update modelview_matrix_
@@ -478,7 +478,7 @@ QGLViewerWidget::rotate( const Vec3f& _axis, float _angle )
 
 
 bool
-QGLViewerWidget::map_to_sphere( const QPoint& _v2D, Vec3f& _v3D )
+QGLViewerWidget::map_to_sphere( const QPoint& _v2D, OpenMesh::Vec3f& _v3D )
 {
   if ( (_v2D.x() >= 0) && (_v2D.x() <= width()) &&
        (_v2D.y() >= 0) && (_v2D.y() <= height()) ) 
@@ -541,7 +541,7 @@ QGLViewerWidget::view_all()
 
 
 void
-QGLViewerWidget::set_scene_pos( const Vec3f& _cog, float _radius )
+QGLViewerWidget::set_scene_pos( const OpenMesh::Vec3f& _cog, float _radius )
 {
   center_ = _cog;
   radius_ = _radius;
diff --git a/src/OpenMesh/Apps/Unsupported/Streaming/Client/QGLViewerWidget.cc b/src/OpenMesh/Apps/Unsupported/Streaming/Client/QGLViewerWidget.cc
index 797721b7..b04157f7 100644
--- a/src/OpenMesh/Apps/Unsupported/Streaming/Client/QGLViewerWidget.cc
+++ b/src/OpenMesh/Apps/Unsupported/Streaming/Client/QGLViewerWidget.cc
@@ -428,7 +428,7 @@ void QGLViewerWidget::keyPressEvent( QKeyEvent* _event)
 
 
 void
-QGLViewerWidget::translate( const Vec3f& _trans )
+QGLViewerWidget::translate( const OpenMesh::Vec3f& _trans )
 {
   // Translate the object by _trans
   // Update modelview_matrix_
@@ -444,7 +444,7 @@ QGLViewerWidget::translate( const Vec3f& _trans )
 
 
 void
-QGLViewerWidget::rotate( const Vec3f& _axis, float _angle )
+QGLViewerWidget::rotate( const OpenMesh::Vec3f& _axis, float _angle )
 {
   // Rotate around center center_, axis _axis, by angle _angle
   // Update modelview_matrix_
@@ -476,7 +476,7 @@ QGLViewerWidget::rotate( const Vec3f& _axis, float _angle )
 
 
 bool
-QGLViewerWidget::map_to_sphere( const QPoint& _v2D, Vec3f& _v3D )
+QGLViewerWidget::map_to_sphere( const QPoint& _v2D, OpenMesh::Vec3f& _v3D )
 {
   if ( (_v2D.x() >= 0) && (_v2D.x() <= width()) &&
        (_v2D.y() >= 0) && (_v2D.y() <= height()) ) 
@@ -539,7 +539,7 @@ QGLViewerWidget::view_all()
 
 
 void
-QGLViewerWidget::set_scene_pos( const Vec3f& _cog, float _radius )
+QGLViewerWidget::set_scene_pos( const OpenMesh::Vec3f& _cog, float _radius )
 {
   center_ = _cog;
   radius_ = _radius;
diff --git a/src/OpenMesh/Core/Utils/Property.hh b/src/OpenMesh/Core/Utils/Property.hh
index b8a10598..824eb82c 100644
--- a/src/OpenMesh/Core/Utils/Property.hh
+++ b/src/OpenMesh/Core/Utils/Property.hh
@@ -206,10 +206,9 @@ private:
 //-----------------------------------------------------------------------------
 
 
-/** \class PropertyT<bool> Property.hh <OpenMesh/Core/Utils/PropertyT.hh>
+/** Property specialization for bool type. 
 
-  Property specialization for bool type. The data will be stored as
-  a bitset.
+  The data will be stored as a bitset.
  */
 template <>
 class PropertyT<bool> : public BaseProperty
@@ -364,9 +363,7 @@ private:
 //-----------------------------------------------------------------------------
 
 
-/** \class PropertyT<std::string> Property.hh <OpenMesh/Core/Utils/PropertyT.hh>
-
-  Property specialization for std::string type.
+/** Property specialization for std::string type.
 */
 template <>
 class PropertyT<std::string> : public BaseProperty
diff --git a/src/OpenMesh/Tools/Utils/Timer.cc b/src/OpenMesh/Tools/Utils/Timer.cc
index 370f918b..1f7eb5d3 100644
--- a/src/OpenMesh/Tools/Utils/Timer.cc
+++ b/src/OpenMesh/Tools/Utils/Timer.cc
@@ -83,7 +83,9 @@ public:
 // ------------------------------------------------------------- windows 32 ----
 #if defined(WIN32) && (defined(_MSC_VER) || defined(__INTEL_COMPILER))
 
+#ifndef DOXY_IGNORE_THIS
 #include <windows.h>
+#endif
 
 class TimerImplWin32 : public TimerImpl
 {
@@ -143,7 +145,9 @@ double TimerImplWin32::seconds(void) const
 // ------------------------------------------------------------- posix time ----
 #elif defined(__GNUC__) && defined(__POSIX__) 
 
+#ifndef DOXY_IGNORE_THIS
 #  include <time.h>
+#endif
 
 template <clockid_t N>
 class TimerImplPosix : public TimerImpl