diff --git a/libraries/Filter/Butter.h b/libraries/Filter/Butter.h
index 7c36dcc113..1a49617bc3 100644
--- a/libraries/Filter/Butter.h
+++ b/libraries/Filter/Butter.h
@@ -2,7 +2,7 @@
 #ifndef __FILTER_BUTTER_H__
 #define __FILTER_BUTTER_H__
 
-#include <AP_HAL.h>
+#include <AP_HAL/AP_HAL.h>
 
 template <typename Coefficients>
 class Butter2
diff --git a/libraries/Filter/DerivativeFilter.cpp b/libraries/Filter/DerivativeFilter.cpp
index db4e990ddc..6a86f964ca 100644
--- a/libraries/Filter/DerivativeFilter.cpp
+++ b/libraries/Filter/DerivativeFilter.cpp
@@ -19,9 +19,9 @@
 /// See http://www.holoborodko.com/pavel/numerical-methods/numerical-derivative/smooth-low-noise-differentiators/
 //
 #include <inttypes.h>
-#include <AP_Math.h>
-#include <Filter.h>
-#include <DerivativeFilter.h>
+#include <AP_Math/AP_Math.h>
+#include "Filter.h"
+#include "DerivativeFilter.h"
 
 
 template <class T,  uint8_t FILTER_SIZE>
diff --git a/libraries/Filter/LowPassFilter.h b/libraries/Filter/LowPassFilter.h
index c9cf775331..c551c18537 100644
--- a/libraries/Filter/LowPassFilter.h
+++ b/libraries/Filter/LowPassFilter.h
@@ -23,7 +23,7 @@
 #ifndef __LOW_PASS_FILTER_H__
 #define __LOW_PASS_FILTER_H__
 
-#include <AP_Math.h>
+#include <AP_Math/AP_Math.h>
 #include "FilterClass.h"
 
 // DigitalLPF implements the filter math
diff --git a/libraries/Filter/LowPassFilter2p.cpp b/libraries/Filter/LowPassFilter2p.cpp
index 7ac93b004d..dbd0972dc3 100644
--- a/libraries/Filter/LowPassFilter2p.cpp
+++ b/libraries/Filter/LowPassFilter2p.cpp
@@ -20,7 +20,7 @@
 /// Author: Leonard Hall <LeonardTHall@gmail.com>
 
 #include <inttypes.h>
-#include <AP_Math.h>
+#include <AP_Math/AP_Math.h>
 #include "LowPassFilter2p.h"
 
 float DigitalBiquadFilter::apply(float sample, const struct biquad_params &params)
diff --git a/libraries/Filter/examples/Derivative/Derivative.cpp b/libraries/Filter/examples/Derivative/Derivative.cpp
index 58cb28f943..6721eaf151 100644
--- a/libraries/Filter/examples/Derivative/Derivative.cpp
+++ b/libraries/Filter/examples/Derivative/Derivative.cpp
@@ -3,15 +3,15 @@
  */
 
 #include <stdlib.h>
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Math.h>
-#include <Filter.h>
-#include <DerivativeFilter.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Math/AP_Math.h>
+#include <Filter/Filter.h>
+#include <Filter/DerivativeFilter.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/Filter/examples/Filter/Filter.cpp b/libraries/Filter/examples/Filter/Filter.cpp
index b2a82265d6..8899650b76 100644
--- a/libraries/Filter/examples/Filter/Filter.cpp
+++ b/libraries/Filter/examples/Filter/Filter.cpp
@@ -3,18 +3,18 @@
  *       Code by Randy Mackay and Jason Short. DIYDrones.com
  */
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_Empty.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
-#include <Filter.h>                     // Filter library
-#include <ModeFilter.h>         // ModeFilter class (inherits from Filter class)
-#include <AverageFilter.h>      // AverageFilter class (inherits from Filter class)
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_HAL_PX4/AP_HAL_PX4.h>
+#include <AP_HAL_Empty/AP_HAL_Empty.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Math/AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
+#include <Filter/Filter.h>                     // Filter library
+#include <Filter/ModeFilter.h>         // ModeFilter class (inherits from Filter class)
+#include <Filter/AverageFilter.h>      // AverageFilter class (inherits from Filter class)
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/Filter/examples/LowPassFilter/LowPassFilter.cpp b/libraries/Filter/examples/LowPassFilter/LowPassFilter.cpp
index 9de96aa54f..cd92b2b109 100644
--- a/libraries/Filter/examples/LowPassFilter/LowPassFilter.cpp
+++ b/libraries/Filter/examples/LowPassFilter/LowPassFilter.cpp
@@ -3,15 +3,15 @@
  *       Code by Randy Mackay. DIYDrones.com
  */
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
-#include <Filter.h>                     // Filter library
-#include <LowPassFilter.h>      // LowPassFilter class (inherits from Filter class)
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Math/AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
+#include <Filter/Filter.h>                     // Filter library
+#include <Filter/LowPassFilter.h>      // LowPassFilter class (inherits from Filter class)
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;
 
diff --git a/libraries/Filter/examples/LowPassFilter2p/LowPassFilter2p.cpp b/libraries/Filter/examples/LowPassFilter2p/LowPassFilter2p.cpp
index 465045275a..31b84e9a8d 100644
--- a/libraries/Filter/examples/LowPassFilter2p/LowPassFilter2p.cpp
+++ b/libraries/Filter/examples/LowPassFilter2p/LowPassFilter2p.cpp
@@ -3,17 +3,17 @@
  *       Code by Randy Mackay and Andrew Tridgell
  */
 
-#include <AP_Common.h>
-#include <AP_Progmem.h>
-#include <AP_HAL.h>
-#include <AP_HAL_AVR.h>
-#include <AP_HAL_PX4.h>
-#include <AP_HAL_FLYMAPLE.h>
-#include <AP_Param.h>
-#include <StorageManager.h>
-#include <AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
-#include <Filter.h>                     // Filter library
-#include <LowPassFilter2p.h>
+#include <AP_Common/AP_Common.h>
+#include <AP_Progmem/AP_Progmem.h>
+#include <AP_HAL/AP_HAL.h>
+#include <AP_HAL_AVR/AP_HAL_AVR.h>
+#include <AP_HAL_PX4/AP_HAL_PX4.h>
+#include <AP_HAL_FLYMAPLE/AP_HAL_FLYMAPLE.h>
+#include <AP_Param/AP_Param.h>
+#include <StorageManager/StorageManager.h>
+#include <AP_Math/AP_Math.h>            // ArduPilot Mega Vector/Matrix math Library
+#include <Filter/Filter.h>                     // Filter library
+#include <Filter/LowPassFilter2p.h>
 
 const AP_HAL::HAL& hal = AP_HAL_BOARD_DRIVER;