The layer-by-layer assembly of poly(diallyldimethylammonium chloride) and poly(sodium 4-styrenesulfonate) is studied on templates with imprinted arrays of microwells ranging from 2 to 25 mu m and different aspect ratios. The thickness and microstructure of polyelectrolyte multilayers (PEMs) are measured using scanning electron microscopy. At 0.2 M ionic strength, the PEM film evenly coats the template both inside and outside the microwells. If the film is thinner than the critical value of about 400 nm, PEM microstructures collapse upon dissolving the template. Euler's model of critical stress is used to describe the collapse. At 2 M ionic strength, a substantially thinner PEM film is assembled inside the 25 mu m wells than outside. If the well diameter is reduced to 7 and 2 mu m, a much thicker PEM film is formed inside the microwells. These observations have been attributed to the changing of polyelectrolyte conformation in the solutions.