You can add rules to your root Makefile in order to compile the necessary cpp files in other directories. The Makefile example below should be a good start in getting you to where you want to be.
CC=g++ TARGET=cppTest OTHERDIR=../../someotherpath/in/project/src SOURCE = cppTest.cpp SOURCE = $(OTHERDIR)/file.cpp ## End sources definition INCLUDE = -I./ $(AN_INCLUDE_DIR) INCLUDE = -I.$(OTHERDIR)/../inc ## end more includes VPATH=$(OTHERDIR) OBJ=$(join $(addsuffix ../obj/, $(dir $(SOURCE))), $(notdir $(SOURCE:.cpp=.o))) ## Fix dependency destination to be ../.dep relative to the src dir DEPENDS=$(join $(addsuffix ../.dep/, $(dir $(SOURCE))), $(notdir $(SOURCE:.cpp=.d))) ## Default rule executed all: $(TARGET) @true ## Clean Rule clean: @-rm -f $(TARGET) $(OBJ) $(DEPENDS) ## Rule for making the actual target $(TARGET): $(OBJ) @echo "=============" @echo "Linking the target $@" @echo "=============" @$(CC) $(CFLAGS) -o $@ $^ $(LIBS) @echo -- Link finished -- ## Generic compilation rule %.o : %.cpp @mkdir -p $(dir $@) @echo "=============" @echo "Compiling $<" @$(CC) $(CFLAGS) -c $< -o $@ ## Rules for object files from cpp files ## Object file for each file is put in obj directory ## one level up from the actual source directory. ../obj/%.o : %.cpp @mkdir -p $(dir $@) @echo "=============" @echo "Compiling $<" @$(CC) $(CFLAGS) -c $< -o $@ # Rule for "other directory" You will need one per "other" dir $(OTHERDIR)/../obj/%.o : %.cpp @mkdir -p $(dir $@) @echo "=============" @echo "Compiling $<" @$(CC) $(CFLAGS) -c $< -o $@ ## Make dependancy rules ../.dep/%.d: %.cpp @mkdir -p $(dir $@) @echo "=============" @echo Building dependencies file for $*.o @$(SHELL) -ec '$(CC) -M $(CFLAGS) $< | sed "s^$*.o^../obj/$*.o^" > $@' ## Dependency rule for "other" directory $(OTHERDIR)/../.dep/%.d: %.cpp @mkdir -p $(dir $@) @echo "=============" @echo Building dependencies file for $*.o @$(SHELL) -ec '$(CC) -M $(CFLAGS) $< | sed "s^$*.o^$(OTHERDIR)/../obj/$*.o^" > $@' ## Include the dependency files -include $(DEPENDS)