The optimized conditions for the cross-sectional TEM sample preparation using tripod polisher and ion-beam miller was confirmed by AFM and TEM. For the TEM observation of interfaces including InGaN layers like InGaN/GaN MQW structures, the sample preparation by the only tripod polishing was useful due to the reduction of artifacts. On the other hand, in case of the thick nitride films like ELO, PE, and superlattice, both tripod polishing and controlled ion-beam milling were required to improve the reproducibility. As a result, the ion-beam milling with the $60^{circ}$modulation showed the minimum height difference between film and sapphire interface and the ion-beam milling of the $80^{circ}$modulation showed the broad observable width.