The invention includes a method for reducing noise in migration of seismic data, particularly advantageous for imaging by simultaneous encoded source reverse-time migration (SS-RTM). One example embodiment includes the steps of obtaining a plurality of initial subsurface images; decomposing each of the initial subsurface images into components; identifying a set of components comprising one of (i) components having at least one substantially similar characteristic across the plurality of initial subsurface images, and (ii) components having substantially dissimilar characteristics across the plurality of initial subsurface images; and generating an enhanced subsurface image using the identified set of components. For SS-RTM, each of the initial subsurface images is generated by migrating several sources simultaneously using a unique random set of encoding functions. Another embodiment of the invention uses SS-RTM for velocity model building.