Generation of treatment recommendations for topographic-based excimer laser surgical procedures is described that includes generating accurate cylinder compensation and spherical compensation values that are adjusted to compensate for unique characteristics of topographic-based excimer laser surgical systems. Generating treatment recommendations generally includes determining a topographic vector, a posterior astigmatism vector and an anterior astigmatism vector, and generating an internal astigmatism vector using the topographic vector, the posterior astigmatism vector, the anterior astigmatism vector, and a manifest astigmatism vector. In embodiments, the cylinder compensation is generated using multiple vectors while subtracting the internal astigmatism vector and the posterior astigmatism vector which remain in the eye after treatment, and the spherical compensation is generated using an initial spherical compensation modified by addback modifiers and a regression analysis nomogram. In procedures where the corneal epithelium is removed, an epithelial refractive vector is determined from an epithelial thickness/topography map and added to the other vectors.
