Abstract-We present a holistic system for automating the motion of a rolling microrobot for protein crystal harvesting. The RodBot, which was introduced in previous work, is able to perform noncontact manipulation of microscopic objects such as fragile crystals by trapping them in an induced vortex fluid flow. Here, we are concerned with navigating the RodBot autonomously in a liquid environment containing obstacles such as crystals. A literature review shows existing approaches to untethered microrobot control are limited and cluttered environments are often not considered. We demonstrate real-time tracking of the RodBot and surrounding obstacles, kinematic obstacle-free path planning, and nonholonomic path following. The system was evaluated in qualitative and quantitative experiments, shows satisfactory performance, and presents itself as a first step towards fully automated crystal harvesting.