Brake cleaner is a good choice. It will cut most any petroleum based residue. Compressed air will help too. Spray the cleaner deep into the void you're trying to fill then blow it out with air. Do this a couple of times and make sure you don't see any black tracing coming out before filling with whatever product you decide to use.
Just a question but are you sure this hole you're seeing goes all the way through to the crankcase. It could just be a surface imperfection that isn't allowing air to pass. Are you seeing symptoms of a vacuum leak such as a high idle speed, loss of power, hard starting?
Tom