SEF URLS & 404 Pages

Now that i have finally integrated SEF-URLs on my page, i don't know if it it possible to exclude certain URLs from being rewritten. There are a lot of outdated links pointing to my site. I did setup a custom 404 error page, so once in a while even google recognizes they do not exist anymore. Now with SEF-URLs active, all these old URLs get redirected to PHPNS error page (article not found). I guess, this way all the googles will never remove these URLS from their index. Can i exclude for exmple everything that ends with .html or .php from being rewritten?