Methods and apparatus to automatically fabricate fillers are disclosed. An example method includes aligning rigid surface data with flexible surface data, the rigid surface data and the flexible surface data being permitted to overlap when aligned; when aligned, defining the rigid surface data and the flexible surface data based on a same parameter space; calculating a displacement function based on differences between corresponding ones of first points in the flexible surface data and second points in the rigid surface data; determining a modified position of a first one of the first points by modifying the first one of the first points based on a value of the displacement function; calculating a gap between the modified position of the first one of the first points and a second one of the second points; and creating a physical filler to fill a physical gap corresponding to the calculated gap.