By adding a point defect to a photonic crystal structure, a microcavity can be made to trap electromagnetic energy with wavelength inside the photonic bandgap (PBG). This property together with other unique properties of photonic crystals enables us to control the propagation and spectrum of transmitted wave inside the photonic crystal waveguiding structures and to design and implement microscale optical filters. In this paper we focus on the design of notch filters in photonic crystal waveguides based on the coupling of waveguide and cavity. We discuss about the properties of a single cavity and its necessary modifications to achieve efficient coupling between cavity and waveguide and eventually obtain desired notch filters at the frequency range of interest. We also discuss the coupling of multi-cavities to a waveguide and the possibility of attaining filters with better performances is presented, and the spectrum and lineshapes of the resulting filters are characterized.