Talk to your cadre about the timeline. Yes, you can get it done in ROTC, but after you contract. You will get a sheet from your cadre that you'll need to bring in for every appointment: pre-op measurements, 1 month post-op, 2 months post-op, 3 months post-op, 6 months post-op, and a year post-op. I believe you need to have this done a year before a FC1 or six months before FT. (If between 6-12 months, you can get a waiver for FT; if under 6 months, you cannot.)
You will take the sheet with you to your pre-op appointment and get that filled out, but BEFORE you have the surgery, you need to return that sheet to your cadre. They will send it up the chain to HQ AETC/SG, and they need to approve that you can have the surgery. Only then can you move forward.
This is up to date as of December 2013, but could change at any point so the bottom line is, talk to your cadre and double or triple check everything you do. The last thing you want to do is medically disqualify yourself!
(I'm a contracted AS200 who just had PRK surgery in November.)