To morph between two live-action clips, you have to define the source and destination meshes for the front and back clips for the duration of the clips—since the objects change shape and location in each frame of the clips. You can use the Stabilizer to track the movement of the objects and source interpolation to create a smooth morph.
The following illustration shows the source and destination meshes needed to morph a square into a circle, both moving from the upper-left to the lower-right corner of the image window.