In this context, "to bother" has a range of meanings, from mild inconvenience to harassment. In a polite context in England, if you want to check if you are disturbing someone from their work, you could say: "If it's not too much bother, would you mind e.g. doing this for me?" If you get the feeling that they are being nice by helping you but, really, they need to do something else, you can say something like: "You probably need to get on so I won't bother you any longer. Thank-you for your help etc." If the other person is, in fact, totally OK about helping you, they can then correct you. If you ask : "Am I bothering you?" a nice person won't want to admit it, so the question may be a bit too direct. People in other English-speaking countries may speak in a more direct way. But the phrases in my answer are polite enough for any country.

Am I disturbing you?