My doe was extremely timid when I got her, so much so that I couldn't even touch her. I spent a lot of time with her, most of the time I wasn't touching her at all, I sat in the run with her for hours on end and let her run to me and check me out, never did I even attempt to touch her. Then I gradually started carrying treats and I'd hold them in my hand and he's take them. When she would do that, I would start introducing movements so instead of holding the treat in her reach, I would have to move my hand towards her so she could have it. She got used to me moving pretty soon.
After that I started petting her while feeding her and pretty soon I could touch her without having to feed her. I also made sure I only touched her when she wanted to be, she would sit on top the little wooden hutch/box in the run and that was the only place I would touch her for a while, she soon realised that unless she was on that box, I wouldn't touch her. She was soon used to it and I was able to touch her anywhere, but I maintained the box as a marker. It was the only place I'd pick her up from, if she didn't want to go in, she wouldn't go on it. I even managed to voice train her through all this and she would jump on the box when I said "box".
All that took about 4 months to really accomplish and a lot of patience. Take things slowly and let the rabbit tell you when it's ready, rushing things only makes it take a lot longer in the end.
Anyways, good luck!
P.S.- Even though I didn't spend a lot of time touching her, I made sure to handle her EVERY day. I would put her on her back and play with her feet and mouth to make sure that vet visits, nail trimming, and other things were very easy to do. You should be able to look over her very thoroughly by the end of it, and it's easiest when they're young.
