the thing is that noise generally is random. However, in your case it may not be completely random.
That said, you can't subtract noise, except in cases in which it isn't random, i.e. if you deal with a temporally stable background.
You really should try to take two images without specimen and subtract them. If the result isn't zero or near zero, you have a random component in your background and you must use different methods to get rid of it.