Two types of cells--human platelets and spore cells--were encapsulated in polymer shells by adsorbing polyanions and polycations in a stepwise fashion. The encapsulated cells were attached to gold and silicon surfaces and their morphological and adhesion properties were studied in air using tapping mode atomic force microscopy (AFM). The roughness of the encapsulated cells increased upon the addition of a new polymer layer. The increase in roughness can be attributed to the formation of a shell around the cells, which is stabilized by electrostatic interactions, as well as to the drying effects associated with the immobilization and dehydration of the cells. Trigger mode was used to perform the force imaging and map out the adhesion characteristics of the cells. Systematic "maps" of the adhesion properties of the encapsulated cells to clean and amine terminated AFM tips were collected. The adhesion force data for the different tips and encapsulated cells showed dependence not only on the number and thickness of the polymer layers, but also on the interactions between these layers. The encapsulated cells' morphology and roughness characteristics remained intact over a substantial storage period. This stability and adhesion properties make them suitable building blocks for the design and construction of biomimetic templates where AFM is used as the primary tool to do the fabrication.