I think there are mainly two ways to file GC under EB2 category. One is NIW (national interest waiver) which does not require labor certification. You can also apply yourself without employer's sponsership in NIW. In the employer sponsered with labor certification, the company has to file for labor certification first based on your current job that must be permanent. If your current position requires only Bachelor's degree, the company has to go for EB3 category no matter what is your current degree. In this situation, either the employer has to assign (or create) you in the position which requires master's degree or you have to file under NIW. But NIW requires various evidences such as research publications, impact on US economy, environment, medical etc from your capacity and job. I have seen several NIW cases approved who has PhD and has several publication. You may need some outstanding record of something to file based on Master's degree.

Best idea would be to consult with an immigration layer and read some information in USCIS website.