Effective in situ, in vivo tumour margin assessment is an important, yet unmet, clinical demand in surgical oncology. Recent advances in probe-based optical imaging tools such as confocal endomicroscopy is making inroads in clinical applications. In practice, maintaining consistent tissue contact whilst ensuring large area surveillance is crucial for its practical adoption and for this reason there is a great demand for robotic assistance so that high-speed endomicroscopes can be combined with autonomous scanning, thus simplifying its incorporation in routine surgical workflows. In this paper, a cooperatively controlled robotic manipulator is developed, which provides a stable mechatronically-enhanced platform for micro-scanning tools to perform local high resolution mosaics over 3D undulating moving surfaces. Detailed kinematic and overall system performance analyses are provided and the results demonstrate the adaptability in terms of both contact force and orientation control of the system, and thus its simplicity in practical deployment and value for clinical adoption.