We propose a process for the fabrication of defects, such as waveguides and resonators, embedded in a three-dimensional photonic crystal. The method is both efficient and flexible. It allows for arbitrary placement of defects within a high quality photonic crystal lattice of arbitrary symmetry, and achieves that in a minimum number of steps. Our approach relies on the exploitation of particular advantages of different types of lithography. Accordingly, we use ultraviolet interferometric (holographic) lithography to define the three-dimensional lattice of the photonic crystal in a thick layer of photoresist. This method is extremely efficient, requiring only a few nanosecond-long pulses of a high power UV laser to expose areas as large as several square centimeters. In order to pattern waveguides and cavities, we use electron beam lithography. Here we take advantage of a finite penetration depth of electrons in the material. How,deep an area is exposed is determined by the voltage accelerating the electrons striking the resist layer. Thus, the height of the patterned waveguides can be precisely controlled. The procedure depends on the existence of resists sensitive to both ultraviolet radiation and electron beam, such as SU8 as well as AZ5200.