Generally yes that is what removal tools are for, to be run in safe mode for removal of stubborn programs but can also be used to clean up leftovers. Iv used MSE 2 and it does leave remnants all though the computer, check program data, the roaming file, numerus microsoft files and in the registry - software keys and software/microsoft, so it does pay to run the tool for MSE just to be safe and still check through the system for anymore as should be done with any av or security product, the removal tool downloads are only a couple of hundred Kb and very quick to run so imo it is hassle free safe practice.