I believe you can, there's specific code in the cgminer repo for antminer s3:
http://ck.kolivas.org/apps/cgminer/antminer/s3/Your setup will be a little bit dependent on your platform, on linux, I usually just download the source for cgminer and do "./configure && make && sudo make install". And sometimes there's some option for ./configure which you want to use to make sure that you're supporting your specific miner hardware.
Probably you should go ahead and get started and post back here when/if you actually get stuck.