Monodisperse emulsion droplets with a high volume fraction form crystalline phases that can potentially serve as adjustable photomasks in photolithography. Such photomasks were prepared using a microfluidic device in which a flow-focusing junction, side channels, and a reservoir were connected in series. Transparent oil droplets were generated in a dye-containing continuous water phase at the flow-focusing junction. The droplets were then concentrated through the selective removal of the continuous phase using the side channels. This process led to the formation of a regular array of droplets in the reservoir with a configuration that depended on the relative height of the reservoir to the droplet diameter. The configurations could be selected among a single-layered hexagonal array, a bilayered square array, and a bilayered hexagonal array. The droplet arrays were used as a photomask to create hexagonal or square arrays of microdots. The transmittance profile of the ultraviolet (UV) light from each droplet was parabolic, which enabled the dot size to be tuned by controlling the UV irradiation time. This mask effect is otherwise difficult to achieve using conventional photomasks. The dot size and array periodicity could be adjusted by the in-situ control of the droplet size at the flow-focusing droplet maker. The combination of droplet size adjustments and the UV irradiation time provided independent control over the dot size and array periodicity to enable the preparation of a series of hexagonal microarrays with a wide spectrum of array parameters using a single microfluidic device.