Atomic force microscopy (AFM) in conjunction with cross-section analysis was applied to determine the distribution, position and contact angle of spray-deposited water micro-droplets on micro-structured arrays. For this investigation, two micro-structured arrays on silicon wafers with a chessboard pattern of depressions and protrusions of various sizes were manufactured by e-beam lithography. The first array had a silicon oxide/silicon structure (hydrophilic/hydrophilic) with an elevated silicon oxide layer of 40 nm and the second had a gold/silicon structure (hydrophobic/hydrophilic) with an elevated gold layer of 35 nm. On the first array with only hydrophilic surfaces, the behavior of the water droplets was mainly affected by topography, whereby the contact angles on the structures were considerably higher than the contact angles of droplets on unstructured reference surfaces. On the second array the water micro-droplets were confined in the hydrophilic depressions by the hydrophobic boundary whereby the highest contact angle was measured on the smallest squares and the lowest contact angle was found on the largest squares, with the droplet angles of the squares of 1 and 0.5 µm exceeding the contact angles of the droplets on the unstructured reference materials.