Hi Farnoosh,
is it currently working Sen2Cor in the command line? Please try: L2A_Process -h
If the output is this, sen2cor is properly installed:
In this case, to see which installation are you using, please try in the command line: where L2A_Process
If your output starts with: C:\Program Files\Anaconda2\ , then try to set the system variables
PYTHON_BIN = C:\Program Files\Anaconda2\python.exe
SEN2COR_BIN = C:\Program Files\Anaconda2\Lib\site-packages\sen2cor-2.3.0-py2.7.egg\sen2cor
If your output starts with: C:\Users\KOWSAR\Anaconda2\ , then try to set the system variables
PYTHON_BIN = C:\Users\KOWSAR\Anaconda2\python.exe
SEN2COR_BIN = C:\Users\KOWSAR\Anaconda2\Lib\site-packages\sen2cor-2.3.0-py2.7.egg\sen2cor
After that, please, uninstall and re-install the sen2cor plugin in SNAP.
If Sen2Cor is not working in the command line, I think that it is better to uninstall all the anacondas and sen2cor and make a clean installation.