We report on a method to create multiple waveguides simultaneously in 3D in fused silica. A combination of adaptive beam shaping with femtosecond laser writing is used to write two waveguides with changing separation and depth. The method is based on a programmable phase modulator and a dynamic variation of the phase-pattern during the writing process. The depth difference can be dynamically varied by changing a chirp parameter of the applied phase grating pattern. It can be employed in various photonic devices such as couplers, splitters and interferometers. Here we demonstrate splitters with both outputs ending in different depth.