Ultrafast lasers, emitting ultra-short pulses of light, generally of the order of femtoseconds to ten picoseconds, are widely used in micro-processing with the advantage of very little thermal damage. Parallel micro-processing is seen significant developments in laser fabrication, thanking to the spatial light modulator (SLM) which can concert single beam to multiple beams through computer generate holograms (CGHs). However, without synchronization control, on the conditions of changing different holograms or processing on large area beyond scanning galvo’s ability, the fabrication will be interrupted constantly for changing holograms and moving the stages. Therefore, synchronization control is very important to improve the convenience and application of parallel micro-processing. A synchronization control method, carried out through two application software: SAMLight (or WaveRunner) and Labview, is presented in this paper. SAMLight is used to control the laser and the scanning galvo to implement microprocessing, and the developed program with Labview is used to control the SLM and motion stages. The synchronization signals, transmitted between the two software, are utilized by a National Instruments (NI) device USB-6008. Using optimal control methods, the synchronized system can easily and automatically accomplish complicated fabrications with minimum time. A multi-drilling application is provided to verify the affectivity of the synchronized control method. It uses multiple annular beams, generated by superimposing multi-beam CGH onto a diffractive axicon CGH, to drill multiple holes at one time, and it can automatically finish different patterns based on synchronization control. This drilling way is an optical trepanning and it avoids huge laser energy waste with attenuation. The multi-beam CGHs, generated by the Grating and Lens algorithm, are different for different patterns. The processing is over 200 times faster than traditional mechanical trepanning, moving a small laser spot in a larger orbit.