diff --git a/Makefile.inc b/Makefile.inc
index 68b45233524..0d26f9c0961 100644
--- a/Makefile.inc
+++ b/Makefile.inc
@@ -1,7 +1,7 @@
 PROJECT_BASE ?= $(shell pwd)
 ARCH?=x86
 
-export ARCH VPFILE QEMU_EXTRA_FLAGS
+export ARCH VPFILE QEMU_EXTRA_FLAGS PROJECT_BASE
 
 ifdef BSP_VARIANT
 VARIANT_STR=_$(BSP_VARIANT)
@@ -25,21 +25,19 @@ SOURCE_DIR=$(PROJECT_BASE)/src/
 export SOURCE_DIR
 endif
 
+O ?= $(PROJECT_BASE)/outdir
+
 CONFIG_SHELL := $(shell if [ -x "$$BASH" ]; then echo $$BASH; \
 	  else if [ -x /bin/bash ]; then echo /bin/bash; \
 	  else echo sh; fi ; fi)
 
-all: $(CONFIG_DEPS)
-	$(Q)$(MAKE) -C $(TIMO_BASE)  O=$(PROJECT_BASE) \
+all: $(CONFIG_DEPS) $(O)/.dir
+	$(Q)$(MAKE) -C $(TIMO_BASE)  O=$(O) \
 	PROJECT=$(PROJECT_BASE) SOURCE_DIR=$(SOURCE_DIR) CFLAGS=$(CFLAGS)
 
-rm-files:= final-linker.cmd linker.cmd modules.order \
-	staticIdt.o System.map *kernel.lnk \
-	*kernel.map *kernel.elf qemu.pid \
-	.tinymountain.cmd
+rm-files:= .config
 rm-objects:= *.o
-rm-dirs := arch drivers include kernel lib misc \
-	scripts source net .tmp_versions
+rm-dirs := $(O)
 
 cmd_clean_inner_files = \
 	 $(shell cd $(PROJECT_BASE);rm $(rm-files) -f; rm $(rm-dirs) -rf)
@@ -61,25 +59,30 @@ mrproper: FORCE
 	$(Q)$(MAKE) -C $(TIMO_BASE) \
 	PROJECT=$(PROJECT_BASE) mrproper
 
-%config: FORCE
-	$(Q)$(MAKE) -C $(TIMO_BASE) O=$(PROJECT_BASE) \
+%config: $(O)/.dir FORCE
+	$(Q)$(MAKE) -C $(TIMO_BASE) O=$(O) \
 	PROJECT=$(PROJECT_BASE) $@
 
-qemu: $(CONFIG_DEPS)
-	$(Q)$(MAKE) -C $(TIMO_BASE) O=$(PROJECT_BASE) \
-	PROJECT=$(PROJECT_BASE) SOURCE_DIR=$(SOURCE_DIR) qemu
+qemu: $(CONFIG_DEPS) $(O)/.dir
+	$(Q)$(MAKE) -C $(TIMO_BASE) O=$(O) \
+	PROJECT=$(PROJECT_BASE) SOURCE_DIR=$(SOURCE_DIR) CFLAGS=$(CFLAGS) qemu
 
-initconfig:
+initconfig: $(O)/.dir
 	set -e;
-	$(Q)test -s .config || $(Q) $(MAKE) -C $(TIMO_BASE) O=$(PROJECT_BASE) \
+	$(Q)test -s $(O)/.config || $(Q) $(MAKE) -C $(TIMO_BASE) O=$(O) \
 	PROJECT=$(PROJECT_BASE) defconfig
 ifneq (($strip $(CONF_FILE)),)
 	$(Q)$(CONFIG_SHELL) $(TIMO_BASE)/scripts/kconfig/merge_config.sh \
-	-m -O $(PROJECT_BASE) $(PROJECT_BASE)/.config $(CONF_FILE)
+	-m -O $(O) $(O)/.config $(CONF_FILE)
 endif
-	$(Q)yes "" | $(MAKE) -C $(TIMO_BASE) O=$(PROJECT_BASE) \
+	$(Q)yes "" | $(MAKE) -C $(TIMO_BASE) O=$(O) \
 	PROJECT=$(PROJECT_BASE) oldconfig
 
+%/.dir:
+	set -e;
+	$(Q)test -s $(abspath $(dir $@)) || $(Q)mkdir $(abspath $(dir $@))
+	@touch $@
+
 help:
 	$(Q)$(MAKE) -C $(TIMO_BASE) help
 
@@ -87,3 +90,4 @@ PHONY += FORCE clean mrproper
 FORCE:
 
 .PHONY: $(PHONY)
+.PRECIOUS: %/.dir
diff --git a/samples/microkernel/benchmark/app_kernel/src/Makefile b/samples/microkernel/benchmark/app_kernel/src/Makefile
index 6a22128edc1..cc2356bcc65 100644
--- a/samples/microkernel/benchmark/app_kernel/src/Makefile
+++ b/samples/microkernel/benchmark/app_kernel/src/Makefile
@@ -1,5 +1,5 @@
 EXTRA_CFLAGS += -I$(CURDIR)/misc/generated/nodes
-EXTRA_CFLAGS += -I$(CURDIR)/../latency_measure/src
+EXTRA_CFLAGS += -I$(CURDIR)/../../latency_measure/src
 
 obj-y := fifo_b.o mailbox_b.o master.o mempool_b.o \
 	nop_b.o  pipe_r.o sema_r.o event_b.o \
diff --git a/samples/microkernel/benchmark/sys_kernel/Makefile b/samples/microkernel/benchmark/sys_kernel/Makefile
index 07a4820130f..ecf56f0fd5f 100644
--- a/samples/microkernel/benchmark/sys_kernel/Makefile
+++ b/samples/microkernel/benchmark/sys_kernel/Makefile
@@ -1,7 +1,7 @@
 PC8253_BSP_VARIANTS=generic_pc pentium4 minuteia
 
 BSP ?= generic_pc
-VPFILE = $(TIMO_BASE)/samples/microkernel/benchmark/sys_kernel/prj.vpf
+VPFILE = prj.vpf
 KERNEL_TYPE = micro
 CONF_FILE = prj_console_$(if $(filter $(BSP),$(PC8253_BSP_VARIANTS)),pc8253,generic).conf
 SOURCE_DIR = $(TIMO_BASE)/samples/nanokernel/benchmark/sys_kernel/src/
diff --git a/scripts/Makefile.preparch b/scripts/Makefile.preparch
index 12072a65fb9..32ff391bdc2 100644
--- a/scripts/Makefile.preparch
+++ b/scripts/Makefile.preparch
@@ -28,13 +28,13 @@ define filechk_prj.vpf
 		i=$$(($$i+1));\
 		done; \
 	fi; \
-	cat $(VPFILE); \
+	cat $(PROJECT_BASE)/$(VPFILE); \
 	cat $(srctree)/config/$(CONFIG_BSP_DIR)/ukernel/config1p.vpf;)
 endef
 
 #Specific source code generation for Viper
 misc/generated/nodes/prj.vpf:	$(srctree)/config/$(CONFIG_BSP_DIR)/ukernel/config1p.vpf \
-				$(VPFILE) \
+				$(PROJECT_BASE)/$(VPFILE) \
 				include/config/auto.conf FORCE
 	$(call filechk,prj.vpf)
 
diff --git a/scripts/sanity_chk/common.defs b/scripts/sanity_chk/common.defs
index 81b3ae68fce..0f707e3dd0c 100644
--- a/scripts/sanity_chk/common.defs
+++ b/scripts/sanity_chk/common.defs
@@ -352,7 +352,7 @@ build_project() {
 	[ $? -eq 0 ] || fail_exit $? $FUNCNAME $LINENO
 
 	if [ x$2 == x ] ; then
-		elf_name=`${LS} ${PRJ_TYPE[$1]}.elf`
+		elf_name=`${LS} outdir/${PRJ_TYPE[$1]}.elf`
 		[ x${elf_name} != "x" ] || \
 			fail_exit $? $FUNCNAME $LINENO "couldn't build ${proj_name}"
 	fi
@@ -408,12 +408,12 @@ qemu_project() {
 	# get QEMU's pid
 	# (wait for QEMU process to be spawned by examining list of tasks
 	# associated with this script's terminal, then grab the pid)
-	while ! [ -f qemu.pid ]
+	while ! [ -f outdir/qemu.pid ]
 	do
 		${SLEEP} 1
 	done
 
-        qemu_pid=$(<qemu.pid)
+        qemu_pid=$(<outdir/qemu.pid)
 
 	# assume execution will fail
 	let RESULT=1
diff --git a/scripts/sanity_chk/footprint_chk b/scripts/sanity_chk/footprint_chk
index a329efed698..09db34d77f6 100755
--- a/scripts/sanity_chk/footprint_chk
+++ b/scripts/sanity_chk/footprint_chk
@@ -243,7 +243,7 @@ main() {
 			${ECHO} "target:    ${BSP_INFO[${cur_proj}]}"
 			${ECHO} "arguments: ${PRJ_ARGS[$cur_proj]}"
 			${ECHO}
-			${SIZE} *.elf
+			${SIZE} outdir/*.elf
 			${ECHO}
 		fi
 	done