First off, if you look or act nervous, people will pick up on it. Walk in like you belong there. It's just clothing after all. If people give you hassle, just tell them a white lie like, "I lost a bet" or "I'm getting it for my girlfriend." Most people won't bother you though. Some might, and some might be aggressive about it, so be careful.
I actually did something extreme to conquer my fear (for the most part)
I had come from a counseling session at my local gender identity center, and I had gone there dressed. When I left, I dressed back as a guy, but for some reason, I decided to keep my forms. (i figured I could put my coat on over them). On my way home I decided I was going to go get some women's cargo pants. I was feeling extra brave after the session, so I figured I might as well go for it. So I stop by a target and sit there in the parking lot for about 45 minutes, working up the courage.
Sure, I could have put my coat on and walked right in, but I wanted to conquer my fear that day. I finally worked up the courage and walked in. It was close to closing, so very few people were shopping. I strode right into the womens department and picked out a pair of Capris(couldn't find cargo pants :\) and I tried them on in the dressing room. I then proceeded to check out and paid for them. When I got back to my car, I allowed myself to breathe. After that little stunt, going in and buying women's clothes while dressed as a man didn't seem like such a big deal.
In fact, I've gotten to the point where I can walk into a specialty bra store and pick out a bra for myself. I even had one fitted a while back...I need to find that bra.
Keep in mind, my little stunt was rather risky. But really, the best advice I can give you for facing your fear is just do it. It gets easier each time you do it. The first time is tough. But just take a deep breath, stay calm, and go for it. If it helps, do it at a store farther from home. Where no one knows you. After all, you'll probably never see those customers ever again and if you do, they probably won't remember you.