Nuclear morphology was examined to assess the general cell morphology after 7 days when the populations were confluent and cell borders were difficult to identify. The nuclear morphology on PEEK and Ti surfaces were very similar in regards to axial ratio (A), whereas the nuclei on the rough acid-etched endoskeleton surface had a significantly lower axial ratio than either the PEEK or smooth Ti surface indicating more circular nuclei on the acid-etched endoskeleton surface. The nuclear area (B) followed a similar trend to axial ratio with the smooth surfaces demonstrating significantly more nuclear area than the rough acid-etched endoskeleton surface. Finally, the orientation of nuclei (C) was assessed establishing 0° as the average orientation direction. The inset provides a plot of the cumulative distribution and clearly demonstrates that PEEK and smooth Ti surfaces were different than the rough, acid-etched endoskeleton surface. Nuclei on PEEK and smooth Ti were grouped very close to 0° indicating that most cells presented an elongated nucleus in the same direction; however, on the acid-etched endoskeleton surface, the nuclei were randomly oriented with only one range, 70–90°, demonstrating a slight increase. The black dotted line in the inset of (C) provides the expected cumulative distribution for random orientation; p values were calculated for each of the three samples with a χ2 test and yielded p values of 10−10, 10−19, and 1.0 for PEEK, Ti, and acid-etched endoskeleton, respectively. Taken together, these results indicated that the aligned spindle morphology observed early on the PEEK and smooth Ti surfaces persists when the stem cells are confluent, and likewise, the random cuboidal/stellate morphology on the acid-etched endoskeleton surface also persists to the confluent cell layer observed after 7 days.