The invention and development of the scanning tunneling microscope (STM) have opened new and original approaches for atomic- and nanometer-scale studies of surfaces. However, its application for imaging biomolecules has to overcome the poor electrical conductivity of biological samples. This article describes an operation mode of the STM that allows high-resolution imaging of hydrated purple membranes and their selective modification. The imaging requires very low currents (below 1 pA) and applied voltages above 5 V. This mode also allows performance of nanometer-scale modifications of the membranes. These modifications are generated by removing the proteins and lipids from a selected region of the membrane. The removal takes place by establishing tip-membrane mechanical contact. This happens when the operating current is above 2 pA. These experiments pose the problem of electron transport through 5-10-nm-thick insulating materials. We propose a model in which the contrast mechanism is controlled by two factors: the electric field at the interface and the transmission through empty states in the membrane. We also compare these results with STM experiments imaging DMA molecules deposited on insulating substrates. There, the contrast is based on the lateral conductivity of water films. © 1997 John Wiley & Sons, Inc.