This document describes the theory and use of a powerful scalar diffraction theory based computer code for calculation of intensity fields due to diffraction of optical waves by two-dimensional planar apertures and lenses. This code is called FESDIF (Finite Element Scalar Diffraction). It is based upon both Fraunhofer and Kirchhoff scalar diffraction theories. Simplified routines for circular apertures are included. However, the real power of the code comes from its basis in finite element methods. These methods allow the diffracting aperture to be virtually any geometric shape, including the various secondary aperture obstructions present in telescope systems. Aperture functions, with virtually any phase and amplitude variations, are allowed in the aperture openings. Step change aperture functions are accommodated. The incident waves are considered to be monochromatic. Plane waves, spherical waves, or Gaussian laser beams may be incident upon the apertures. Both area and line integral transformations were developed for the finite element based diffraction transformations. There is some loss of aperture function generality in the line integral transformations which are typically many times more computationally efficient than the area integral transformations when applicable to a particular problem.