Optical biopsy methods such as probe-based confocal endomicroscopy can provide intraoperative real-time assessment of tumour margins, including during minimally invasive surgery with flexible endoscopes or robotic platforms. Mosaics can be produced by translating the probe across the target, but it remains difficult to scan over a large field of view with a flexible endomicroscope. In this paper, we have developed a novel flexible scanning device for intraoperative endomicroscopy in minimally invasive surgery (MIS). A Schott leached imaging bundle was integrated into the device and enables the approach, via a flexible path, to deep and narrow spaces in the human body that otherwise would not accessible. The proposed device uses a gear-based flexible concentric tube scanning mechanism to facilitate large field-of-view mosaicing. Experimental results show that the device is able to scan different surface trajectories (e.g., a spiral pattern over a hemi-spherical surface). Results from lens tissue paper and porcine liver tissue are demonstrated, illustrating a viable scanning approach for endomicroscopy in MIS.