Apply a deformer to a subdivision surface

When you apply a deformer to a subdivision surface selected as an object, the deformer applies to the base (level 0) vertices. To apply the deformer to a different level, select the vertices at that level and then apply the deformer. You can assign blend shapes to vertices at any level.

If you delete a deformer and cannot switch to Polygon Proxy mode, delete the history or find the input geometry in the dependency graph and delete it.
Be careful if you have deformers on the same part of the surface at different levels. Without parenting, deformer bases can produce double transforms.
Avoid having different levels of vertices in the same deformer. For example, if you create a full crease at level 1 and apply a wire close to the object surface (level 0), then move the wire or its vertices, the effect is very different than if you apply the wire to level 1 vertices.
If the resulting deformation is undesirable, unbind, delete history, and rebind at a finer level.
You may find that not all vertices are moved by a skeleton bound to a subdivision surface at a level finer than 1 because all vertices at the level were not selected or created before binding. To be sure all vertices are selected, go to level 0 or 1, select all vertices, then refine to the required level and select all.
A deformer at level 2 can override the deformation done at level 1. For example, if you have a weighted cluster at level 1 and a blend shape at level 2, the cluster deformation will disappear when the blend shape weight is set to one. Try putting the blend shape at the finest level or on the same level as the other deformers. You can also try changing the order of the deformations.
A deformer at level 1 can move the surface out of a deformer at a finer level (for example, lattices over the same parts of the surface at levels 2 and 3 and in the case of level 2 lattices, it pulls it out of the range of the lattice at level 3).
Switching to Polygon Proxy mode when you have deformers and skeletons on the subdivision surface unbinds the surface and loses weighting.

Creating blend shape and cluster deformers for subdivision surfaces

To create a blend shape for subdivision surfaces, you can either select the object or select vertices on a given level. If you select the object, Maya blends all vertices at all levels of the surface. If you select vertices of a specific level, Maya blends only those vertices.

To create a cluster for subdivision surfaces, you need an extra row of vertices completely surrounding the vertices you want in the cluster. These extra vertices should not be in the cluster itself, but they must exist on the surface. Without the extra row, you will experience problems weighting the vertices in the cluster.