A method for aligning a microlens array in a sensor die to resolve non-symmetric brightness distribution and color balance of the image captured by the sensor die. The method includes performing a pre-simulation to simulate a microlens array alignment in a silicon die and to determine a shrink-factor and de-centering values, calculating the error in a real product's alignment in process and image offset, performing a post simulation based on offset calculation on the real product and re-design of the microlens alignment, and repeating the steps of calculating the error and performing the post-simulation until a satisfactory brightness distribution is obtained. The sensor die has sensor pixels, each pixel comprising a photodiode and a microlens for directing incoming light rays to the photodiode, wherein optical axis of the microlens is shifted with respect to optical axis of the photodiode by a preset amount determined by at least one iteration of alignment process.