diff --git a/hardware/sam/system/libsam/build_gcc/Makefile b/hardware/sam/system/libsam/build_gcc/Makefile
index e04313c71..162c182cf 100644
--- a/hardware/sam/system/libsam/build_gcc/Makefile
+++ b/hardware/sam/system/libsam/build_gcc/Makefile
@@ -10,16 +10,16 @@ all: libchip_sam3s4_gcc_dbg.a libchip_sam3s4_gcc_rel.a
 
 libchip_sam3s4_gcc_dbg.a:
 	@echo --- Making $@
-	@$(MAKE) CHIP=sam3s4 DEBUG=1 $(SUBMAKE_OPTIONS) -f sam3s.mk
+	@$(MAKE) CHIP=sam3s4 DEBUG=1 $(SUBMAKE_OPTIONS) -f sam3.mk
 
 libchip_sam3s4_gcc_rel.a:
 	@echo --- Making $@
-	@$(MAKE) CHIP=sam3s4 $(SUBMAKE_OPTIONS) -f sam3s.mk
+	@$(MAKE) CHIP=sam3s4 $(SUBMAKE_OPTIONS) -f sam3.mk
 
 .PHONY: clean
 clean:
 	@echo --- Cleaning sam3s4 release and debug
-	@$(MAKE) CHIP=sam3s4 $(SUBMAKE_OPTIONS) -f sam3s.mk $@
-	@$(MAKE) CHIP=sam3s4 DEBUG=1 $(SUBMAKE_OPTIONS) -f sam3s.mk $@
+	@$(MAKE) CHIP=sam3s4 $(SUBMAKE_OPTIONS) -f sam3.mk $@
+	@$(MAKE) CHIP=sam3s4 DEBUG=1 $(SUBMAKE_OPTIONS) -f sam3.mk $@
 
 
diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/acc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/acc.o
index d49f8e715..270e17bfa 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/adc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/adc.o
index acc6c1631..64540f2fb 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/async.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/async.o
index 8df6a62bd..29bdffbe0 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/core_cm3.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/core_cm3.o
index f6b82aa50..0419d4327 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/crccu.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/crccu.o
index 514a284bf..81f63c608 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/dacc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/dacc.o
index 13df586c2..0567289cb 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/efc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/efc.o
index 028dd25e9..f82f954a7 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/exceptions.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/exceptions.o
index d60930312..0db86ea54 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/flashd.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/flashd.o
index cc51cc4bc..187b06f10 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pio.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pio.o
index 5a233506c..c8bbe681c 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pio_capture.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pio_capture.o
index 5c5b883af..6ef2f2715 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pmc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pmc.o
index 19a4a4ebb..dbba6a603 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pwmc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/pwmc.o
index 6bf5010c7..bb9c34d24 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/rtc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/rtc.o
index baff268dc..8a6f13a6a 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/rtt.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/rtt.o
index a8631b274..13801f7a5 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/spi.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/spi.o
index 49e803220..bd443efbe 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/spi_pdc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/spi_pdc.o
index 35afed1b3..631035bf4 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/ssc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/ssc.o
index 460335b4d..10b5337fd 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/tc.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/tc.o
index d9324052c..851a2f53d 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/twi.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/twi.o
index dc31128cf..db2463c31 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/twid.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/twid.o
index de8bd2e9c..24c9bd2c5 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/usart.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/usart.o
index 4a4dcdea0..d2059fddb 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/debug_sam3s4/wdt.o b/hardware/sam/system/libsam/build_gcc/debug_sam3s4/wdt.o
index 07f93065a..df0d4f423 100644
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diff --git a/hardware/sam/system/libsam/build_gcc/sam3.mk b/hardware/sam/system/libsam/build_gcc/sam3.mk
index 0340a3a12..41d671bf2 100644
--- a/hardware/sam/system/libsam/build_gcc/sam3.mk
+++ b/hardware/sam/system/libsam/build_gcc/sam3.mk
@@ -18,21 +18,22 @@ OUTPUT_BIN = ../lib
 
 # Libraries
 PROJECT_BASE_PATH = ..
+CMSIS_BASE_PATH = $(PROJECT_BASE_PATH)/../CMSIS/CM3/CoreSupport
 
 #-------------------------------------------------------------------------------
 # Files
 #-------------------------------------------------------------------------------
 
 vpath %.h $(PROJECT_BASE_PATH)/include
-vpath %.c $(PROJECT_BASE_PATH)/source $(PROJECT_BASE_PATH)/cmsis
-vpath %.s $(PROJECT_BASE_PATH)/source $(PROJECT_BASE_PATH)/cmsis
+vpath %.c $(PROJECT_BASE_PATH)/source $(CMSIS_BASE_PATH)
+vpath %.s $(PROJECT_BASE_PATH)/source $(CMSIS_BASE_PATH)
 
 VPATH+=$(PROJECT_BASE_PATH)/source
-VPATH+=$(PROJECT_BASE_PATH)/cmsis
+VPATH+=$(CMSIS_BASE_PATH)
 
 INCLUDES = -I$(PROJECT_BASE_PATH)
 INCLUDES += -I$(PROJECT_BASE_PATH)/include
-INCLUDES += -I$(PROJECT_BASE_PATH)/cmsis
+INCLUDES += -I$(CMSIS_BASE_PATH)
 
 #-------------------------------------------------------------------------------
 ifdef DEBUG
@@ -62,7 +63,7 @@ OUTPUT_PATH=$(OUTPUT_OBJ)_$(CHIP)
 # C source files and objects
 #-------------------------------------------------------------------------------
 C_SRC=$(wildcard $(PROJECT_BASE_PATH)/source/*.c)
-C_SRC+=$(wildcard $(PROJECT_BASE_PATH)/cmsis/*.c)
+C_SRC+=$(wildcard $(CMSIS_BASE_PATH)/*.c)
 
 C_OBJ_TEMP=$(patsubst %.c, %.o, $(notdir $(C_SRC)))
 
@@ -75,7 +76,7 @@ C_OBJ=$(filter-out $(C_OBJ_FILTER), $(C_OBJ_TEMP))
 # Assembler source files and objects
 #-------------------------------------------------------------------------------
 A_SRC=$(wildcard $(PROJECT_BASE_PATH)/source/*.s)
-A_SRC+=$(wildcard $(PROJECT_BASE_PATH)/cmsis/*.s)
+A_SRC+=$(wildcard $(CMSIS_BASE_PATH)/*.s)
 
 A_OBJ_TEMP=$(patsubst %.s, %.o, $(notdir $(A_SRC)))
 
@@ -127,4 +128,4 @@ clean:
 	-@$(RM) $(subst /,$(SEP),$(OUTPUT_BIN)/$(OUTPUT_LIB)).txt 1>NUL 2>&1
 
 # dependencies
-$(addprefix $(OUTPUT_PATH)/,$(C_OBJ)): $(OUTPUT_PATH)/%.o: $(PROJECT_BASE_PATH)/chip.h $(wildcard $(PROJECT_BASE_PATH)/include/*.h) $(wildcard $(PROJECT_BASE_PATH)/cmsis/*.h)
+$(addprefix $(OUTPUT_PATH)/,$(C_OBJ)): $(OUTPUT_PATH)/%.o: $(PROJECT_BASE_PATH)/chip.h $(wildcard $(PROJECT_BASE_PATH)/include/*.h) $(wildcard $(CMSIS_BASE_PATH)/*.h)
diff --git a/hardware/sam/system/libsam/include/SAM3S.h b/hardware/sam/system/libsam/include/SAM3S.h
index 850cdf4e3..1947c6578 100644
--- a/hardware/sam/system/libsam/include/SAM3S.h
+++ b/hardware/sam/system/libsam/include/SAM3S.h
@@ -129,7 +129,7 @@ typedef enum IRQn
  * \brief CMSIS includes
  */
 
-#include "cmsis/core_cm3.h"
+#include <core_cm3.h>
 
 /*@}*/
 
diff --git a/hardware/sam/system/libsam/lib/libchip_sam3s4_gcc_dbg.a b/hardware/sam/system/libsam/lib/libchip_sam3s4_gcc_dbg.a
index 323442f7c..65351dfde 100644
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diff --git a/hardware/sam/system/libsam/lib/libchip_sam3s4_gcc_rel.a b/hardware/sam/system/libsam/lib/libchip_sam3s4_gcc_rel.a
index de29f6de4..946c0e57e 100644
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