RS3 is a general purpose 3D finite element program for civil and mining applications. With fully-coupled Biot theory, RS3 can be used to model embankment consolidation.
See Tutorial 7 for details on how to model embankment consolidation. The tutorial demonstrates a coupled analysis of a road embankment subject to rectangular loading from typical daily traffic.
The Consolidation of Embankment on Soft Clay document illustrates another example. In this case, multiple layers of embankment are constructed on 4 layers of soil.