Electron microscopy techniques are applied to investigate structural properties of GaN layers selectively grown by hydride vapor phase epitaxy on crystalline and amorphous GaN seed layers deposited on (0001)Al2O3 substrates. Optimalization of the growth conditions lead to a reduction both of the stacking fault concentration and c-axis tilting in the laterally grown regions. During the lateral growth threading dislocations from the seed layer bend from vertical direction of propagation. Bending behavior depends on the type of the dislocation and on the shape of the GaN film in the initial stage of the growth. Optical properties of laterally grown regions are correlated with the high point-defect incorporation that is revealed by high-resolution electron microscopy.