Electrochemical scanning probe microscopy is a physical sciences technique that uses a nanoscale physical probe with an electrochemical sensor to map the local chemical activity of interesting substrates, such as carbon nanotubes, graphene and single living cells. These techniques produce measurements of local chemical properties that are unevenly distributed over a surface, then which maps of the local chemical activity can be constructed. Image reconstruction methods, namely PDE-based inpainting, are usually used for restoration of lost or deteriorated parts of photos and videos. We show how to reconstruct local chemical activities using inpainting methods. We compare different techniques, and conclude that heat equation based inpainting suits the purpose best. We also investigate a method to reconstruct the progress of an experiment by applying 3D heat equation inpainting.