Informatica has some KBs on this topic - it's just too much data for Salesforce to process.
And unfortunately no, currently there's no support for extract filters with Salesforce
Similar question was asked on the forum few times already with no good resolution.
My suggestion - try hiding most of the columns and see if that helps (you can hide multiple columns at once).
Literally, just leave couple of columns and if that woks - start adding back columns you need.
I have tried that but with no success.
Thank you for your reply, i will try and explore other possible solutions.