This is an excellent question and answer for formatting internal storage on Android.
After some 2+ years of constantly changing ROMs, I've noticed that my i9100 shows more often than not the message of "your storage is getting full" or whatever it says. It does not work by clearing apps' data or even removing some of them because it ends up showing the warning soon. Also, factory reset has proved not to do much, since it just does a data wipe.
So I have decided to proceed with a format by entering Recovery > Mounts & storage > Format sdcard.
I just want to check first wether I will be able, after the format has finished, to flash CyanogenMod back from the same recovery (having placed it in the external SD card, which I understand is not formatted together with the internal storage) and have it working all ok, or the format will disable me from doing something else.
So my questions are: