Surface morphology studies of GaN and AlGaN grown by metalorganic chemical vapor deposition (MOCVD) have been carried out using atomic force microscopy. The open core dislocation and steps connecting two threading dislocations of opposite direction are commonly observed in undoped and doped GaN. Structural studies on AlGaN epitaxial layers grown on undoped GaN revealed the formation of open-core dislocation with width upto 300 nm. The nanopipes originate From the threading dislocation formed due to large lattice mismatch between sapphire and GaN. The mismatch also leads to high strain in the epilayers resulting in cracking effect at the edges of the hexagonal V-type defect. The self organized quantum dots features on the smooth surface of AlGaN epilaxial layer exhibit the Stranski-Krastanov(SK) mode of island growth.