lake Need to get physical exam?

I went to my doctor a couple of days ago because I was sick and he told me that I needed to get a physical exam soon because I haven't had one in a while. I am a 21 year old male and wanted to know what he will be checking for during the exam? Do I have to undress completely or can I keep some clothes on? Also should I have a rectal exam done as part of the physical exam as well?there