1. A computer implemented method for performing pre-scanning calibration in a digital microscopy system having an objective lens coupled to a line scan camera and a stage for supporting a microscope slide, where one or more processors of the digital microscopy system are programmed to perform steps comprising: determining a plurality of focus points in a scan area of the microscope slide; determining an optimal focal height for each of the plurality of focus points, wherein each focus point comprises a planar location on the microscope slide and a height of the objective lens; identifying at least three focus points to define a first polygonal planar surface; identifying at least three focus points to define a second polygonal planar surface; and combining the first polygonal planar surface and the second polygonal planar surface to create a non-planar focal surface.