Most finite element software packages (e.g. ANSYS or COMSOL) are very suitable even at small scales like MEMS.

For nano or smaller scales, meshing can become really difficult and the simulation could take days to conclude especially if the ratios of some dimensions within your system are large (e.g. Length/thickness >> 100). In that case, you might want to write your FE code using a programming language like Fortran.

Thanks

you can also use ABAQUS for solving FE problems for MEMS.