I would get a second opinion. Yes, it may seem radical to take out a section of your colon for precancerous polyp but, IMO, so does having a colonoscopy every 3 months. Is the GI doc suggesting this timeline or the GP?? Honestly, I'm not sure, based on the little bit of information you have here, that a surgeon would actually do the surgery. If he would consider doing the surgery, I would specifically ask WHY. What would make the surgeon believe that having these polyps necessitates having surgery?? I would also talk to the surgeon and NOT the GP about what his/her followup schedule would be for colonoscopies. Personally, I love my GP and trust her implicitly, but....she wouldn't make the recommendations for me about something like followup scopes. She would trust either the GI or the surgeon to do that.
I would also suggest that you see a board certified colorectal surgeon for this opinion and not just a general surgeon. Here's a link to verify whichever surgeon you see has this certification.http://www.abcrs.org/cgi-bin/search.pl
Usually, for precancerous polyps, unless there are some extenuating circumstances (such as perhaps a strong family history or a history of aggressive types of cancerous tumors, etc.) the followup schedule is more along the lines of every 1-2 years.
Another piece of very important and useful information that I didn't see posted - how many polyps were removed??
Again, talk to the GI doc or a colorectal surgeon and get more than one opinion.