In the present study, analyses of two micro-factory layouts were performed to improve its micro-pump production rate and efficiency. For the purpose of the analysis, the two layouts, Layout A (existing) with five micro machines (including one micro milling machine) and Layout B (proposed) with six micro machines (including two micro milling machines), were constructed in the virtual environment. First, Layout A was simulated to predict the production time and to calculate the production rate and efficiency. The robot-arm waiting time, which was considered as the bottleneck, had a significant effect on the production rate. Second, to alleviate this bottleneck, we introduced, based on the robot-arm reach envelope concept, another micro milling machine to the Layout A, and named this new scheme Layout B. In the results of our analysis, Layout B improved the production rate by about 1.88 times and enhanced the efficiency by a factor of 1.57.