Usually it's as simple as adding a "rm -f *.f" after the compile command. Depends on how the makefile is set up though.
For one of my projects, I have the make command automatically clear out all of the .o files after compilation, so it builds from scratch every time. For that, I have this in my makefile:
$(FC) -o $@ $(OBJS) $(LDFLAGS) $(LIBS)
rm *.o *.mod
Just make damn sure you don't accidentally run a "make" where you actually keep the source