An in-house developed finite-difference time-domain (FDTD) code has been used to simulate certain patterned defects as found in the semiconductor industry. Intrinsic to FDTD is the establishment of a simulation domain, a 3-D matrix of some arbitrary size (X, Y, Z) comprised of smaller cells (in our case, cubic with side length x), with each cell indexed to a material (including the vacuum) to form the geometry. Although the specific text files used as inputs to the in-house FDTD engine are provided, such files are likely incompatible with external FDTD solutions for the replication of our results. Therefore, entire 3-D matrices for our simulations have been reduced to single-vector, readable ASCII data files indexing the geometry and materials of the system, accompanied by text files that supply the optical constants used in the simulation as well as cross-sectional images that allow verification by others of their reconstruction of the 3-D matrix from the supplied 1-D ASCII data files.