I'm female and did a CS Masters, Engineering undergrad. If it's what you enjoy, go for it. It was male dominated in Uni, but my first job after actually had quite a few females, most of them had been there a really long time too. I did have an interview in one place that was very male dominated and had a horrible atmosphere but it was very obvious that was the case at the interview, so there's no way I would have worked there.
I'm trying to work for myself now. The only way I could say I've been treated as an anomaly is in the most complimentary sense in that I am the go to person for advice for anyone who knows me, or even people who know of me and know I can help with computer problems/websites etc.
So don't worry. If it's what you want to do, go for it. The most important thing is doing what you enjoy. It can actually be advantageous being a woman when looking for a job in CS or other male dominated industries if they have to try to have a good gender balance (as I see Sycamores has pointed out too). The people who look at you oddly now are the same people who will be looking at you for help when you're qualified, trust me!
If you have any other questions about it feel free to ask.
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