Applying a patch to a source file is done before make. Since it involves changing the sources so that the final executable behaves differently, it can't be done after the make.
There is a utility called patch that takes a patch file (a partial kernel patch is below) in diff format and applies the changes to your original sources. Have a look at `man patch` for more info.
Here is a simple example that the patch utility will use to remove the line 'EXTRAVERSION = .5' from your original sources and insert the line 'EXTRAVERSION = .6'
Code:
diff --git a/Makefile b/Makefile
index ea6f2f9..8c6fcb0 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
VERSION = 2
PATCHLEVEL = 6
SUBLEVEL = 14
-EXTRAVERSION = .5
+EXTRAVERSION = .6
NAME=Affluent Albatross
# *DOCUMENTATION*
After patching, you can run `./configure && make && make install` or whatever your particular app needs. Alternatively, you can edit the file by hand with a text editor (vi, etc.) and then `./configure && make && make install`