Planar waveguides were fabricated in fused silica and quartz crystal by Cu2+ ion implantation respectively. The guiding mode property was investigated in two types of waveguides by the prism-coupling method. The results indicate that an enhance-type waveguide formed in fused silica, while a barrier-type waveguide formed in quartz crystal by the same ion implantation. The anealing effects to the effective refractive indices of guiding modes in two types of waveguides were researched. The effective refractive indices of the guiding modes in fused silica decrease with the increase of annealing temperature. However, in quartz crystal the effective refractive indices of the guiding modes increase firstly and then decrease with the increase of annealing temperature. In order to investigate the formation mechanism of two kinds of waveguide, the distribution of the electronic and nuclear energy deposition in fused silica and quartz crystal were simulated using the SRIM code. In addition, the refractive index profiles of the types of waveguide were reconstructed. The simulation results show that in fused silica the main reason of the waveguide formation is that the refractive index in the near-surface region is larger than the substrate. However, in quartz crystal waveguide the major formation reason is that the refractive index at the end of ion track is less than the substrate region. Therefore, the electronic energy damage plays an important role for the formation of fused silica waveguide, while nuclear energy deposition is the dominant factor in the quartz crystal waveguide.