Using finite difference time domain (FDTD) simulations, we study waveguide configurations in a three dimensional layer-by-layer photonic crystal. We study waveguides lying in the plane of the rods. These can be created by removing one or more rods from one layer and the wave is propagating along the removed rods. An L-shaped waveguide is created by removing part of a rod in one layer and part of a rod in the next layer. The removed rods are perpendicular to each other. We found that 100 $\%$ transmission efficiency can be achieved through the 90$^o$ bend. Also, waveguides created by removing a whole or a part of a rod from each unit cell along the stacking direction have been studied. In that case the wave is mainly concentrated around the defects. The overlap of the wavefunction of neighboring defects allows the propagation of the wave.