the only thing that you can do is to remove all pixels which were identified as clouds in the automated scene classification done by snap. You can do that in the band properties by creating a valid pixel expression. sen2cor already produced cloud masks which you can use for this, just make sure to display the maks in the band maths as well. Similar as here: Export for unwrapping
I tried to give an example here in another context: Cloud related problem
Some more topics on cloud masking can be found via the search function: https://forum.step.esa.int/search?q=“Cloud masking”