Either the students write their own programs in Fortran, C, etc. which is a time consuming work or with one of the many commercial codes available. The commercial codes can be used without the students understanding the underlying physics and the numeric method the code is built on.
Nothing is hidden on the way.
The Finite Element method is in itself an educational method teaching the applied mechanics area. The method breaks down the problem in simple parts, for which geometry, physical behavior and boundary conditions can easily be described. Analogies between different physical applications are made visible with the method.