We measure two-dimensional (2D) profiles of beam spots in a high-density spot array for a maskless lithography system. Since the size of each spot is comparable to that of a pixel in a charge-coupled device (CCD), we detect image frame data, which are the distribution of the intensity of the spot overlapped on the active area of the pixel in the CCD, by scanning with a nano-stage. Using the image frame data of the scanning CCD we determine reconstructed images of the beam spot array. We calculate the 2D profile of each spot by taking the deconvolution of the reconstructed image of the spot with the active area of the CCD pixel. We theoretically analyze the uncertainty in the measurement of profiles in terms of spot size for the variation of the scanning step of the nano-stage and determine the step size to achieve uncertainty of less than 100nm. We experimentally demonstrate the measurement of profiles of an 11×11 spot array for the proof of concept. Also, we analyze various parameters of the spot array, such as ellipticity, rotation of the spot profile, spot size, intensity distribution, and position.