Remove Mac OS X from secondary hard drive ?

Hi,

I have a MacBook Pro early 2011 2.2 ghz with an SSD and a HDD. Mac OS is currently installed on both hard drives and I would like to remove it from my second hard drive, without deleting all my documents, movies, etc.

I can't use Migration Tool to transfer all my data, because the SSD is only 120GB. If I need to remove the system files manually, please tell which are the ones to delete and how can I access them if they're hidden.

Thanks in advance,

Franklin

Note: my secondary hard drive is the hard drive that apple shipped with computer, I remove the optical drive to install it.