A method for printing a three-dimensional part with an additive manufacturing system, the method comprising: providing a bitslice stack having a plurality of bitslices; printing a plurality of successive layers of the three-dimensional part with the additive manufacturing system based on the bitslice stack; providing one or more sensors for measuring surface heights of the plurality of successive layers measuring surface heights of a first printed layer and each of successive layers to obtain a z-height composite image of each measured layer comprising a plurality of pixels; obtaining predicted stack heights for a bitslice of the plurality of bitslices corresponding to the first printed layer; determining differences between the measured surface heights and the predicted stack heights for each of the plurality of pixels; providing a controller assembly comparing heights from the composite image for each printed layer to the predicted stack height of the associated bitslice to identify one or more topographical error regions based on the determined differences, including comparing the determined differences to a threshold value, wherein the one or more topographical error regions comprise one or more underfilled regions, one or more overfilled regions, or combinations thereof; the controller assembly determines whether a given pixel in composite image has a z-height that is above or below the predicted bitslice height by one bitslice thicknesses or more; the controller assembly determines if the pixel of composite image has a z-height that is below the predicted bitslice height by one bitslice thicknesses or more, then controller assembly identifies that this voxel in the printed layer is underfilled and modifying the bitslice stack to compensate for the one or more topographical error regions; wherein modifying the bitslice stack comprises generating one or more additional bitslices to compensate for the one or more underfilled regions; and introducing the one or more additional bitslices into a frame sequence of the bitslice stack prior to a next pending bitslice of the bitslice stack. providing a bitslice stack having a plurality of bitslices; printing a plurality of successive layers of the three-dimensional part with the additive manufacturing system based on the bitslice stack; providing one or more sensors for measuring surface heights of the plurality of successive layers measuring surface heights of a first printed layer and each of successive layers to obtain a z-height composite image of each measured layer comprising a plurality of pixels; obtaining predicted stack heights for a bitslice of the plurality of bitslices corresponding to the first printed layer; determining differences between the measured surface heights and the predicted stack heights for each of the plurality of pixels; providing a controller assembly comparing heights from the composite image for each printed layer to the predicted stack height of the associated bitslice to identify one or more topographical error regions based on the determined differences, including comparing the determined differences to a threshold value, wherein the one or more topographical error regions comprise one or more underfilled regions, one or more overfilled regions, or combinations thereof; the controller assembly determines whether a given pixel in composite image has a z-height that is above or below the predicted bitslice height by one bitslice thicknesses or more; the controller assembly determines if the pixel of composite image has a z-height that is below the predicted bitslice height by one bitslice thicknesses or more, then controller assembly identifies that this voxel in the printed layer is underfilled and modifying the bitslice stack to compensate for the one or more topographical error regions; wherein modifying the bitslice stack comprises generating one or more additional bitslices to compensate for the one or more underfilled regions; and introducing the one or more additional bitslices into a frame sequence of the bitslice stack prior to a next pending bitslice of the bitslice stack.