A month ago, my pet rabbit lost her life to a horrible case of pneumonia. We had taken her to the hospital, and attempted to begin the healing process, but she soon passed in my arms. A little insight on rabbits: since they are prey animals, if they show any kind of weakness in the wild, then they will be killed quickly. Since it was her instinct to hide her illness from me, she was sick for some time it seems. I'm worried that the corner I kept her in would possibly be contaminated. I cleaned up everything that she wasn't in direct contact with, or was nearby enough to infect. So, things like her hutch, food dish, water bottle, were all thrown away. I'm worried that there are still microbes living in the carpeting of her corner. Would the microbes still be in the carpeting? Could I possibly infect a pet I bring home now and keep in the same area? I vaccumed the carpet as best I could and cleaned up any urination spots that were there, but I'm still not sure.

Most bacteria will last for a few hours no more. If a virus possibly a day or so. From what you say and the cleaning you have done I do not think you need to worry about transfer of infection if you buy a new healthy rabbit.