Super-resolution imaging techniques reconstruct a high resolution image from a set of low resolution images that are taken from almost the same point of view. The problem can be subdivided into two main parts: an image registration part where the different input images are aligned with each other, and a reconstruction part, where the high resolution image is reconstructed from the aligned images. In this paper, we mainly consider the first step: image registration. We present three frequency domain methods to accurately align a set of undersampled images. First, we describe a registration method for images that have an aliasing-free part in their spectrum. The images are then registered using that aliasing-free part. Next, we present two subspace methods to register completely aliased images. Arbitrary undersampling factors are possible with these methods, but they have an increased computational complexity. In all three methods, we only consider planar shifts. We also show the results of these three algorithms in simulations and practical experiments.