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Recent advances in telepathology, telemicroscopy, and telemedicine have opened new avenues for collaboration in medical care and scientific research. Such technology allows remote scientists and physicians to visualize and investigate biological samples in real-time. Imaging of biological specimens requires micro and even nano-scale resolution for which atomic force microscope (AFM) provides unprecedented capabilities. However, AFM has some limitations in particular, the probing hardware of AFM can introduce noise in the captured images. Robust image processing techniques are needed for accurate nano-scale representation and visualization of images generated by AFM. In this paper, we present a real-time architecture for an integrated remote AFM-based imaging system. The proposed architecture allows real-time control of a remotely located AFM and enables capturing, processing and communication of AFM images over the network. The architecture consists of four major components including, a remote AFM and real-time controller module, an image processing module for real-time image correction, a client system for visualization of scanned biological images, and a distributed image database system for information retrieval, classification, and archiving of biological specimen images received from remote AFM.