A method of operating a selective deposition based additive manufacturing system capable of producing a three-dimensional (3D) part includes developing a first layer using at least one electrostatography engine, transfusing the first layer on a part build surface using a transfusion assembly to build the 3D part in a layer-by-layer manner on a part build platform such that a portion of the first layer further builds a fiducial structure in a layer-by-layer manner on the part build platform, measuring a height of the fiducial structure, computing an error between the measured height of the fiducial structure and a target height, adjusting a parameter of the at least one electrostatography engine as a function of the error, developing a second layer using the at least one electrostatography engine in accordance with the adjusted parameter, and transfusing the second layer using the transfusion assembly to further build the 3D part.