I am looking for a way to apply a transformation matrix to only one side of an extruded shape. The easiest way appears to be to “applymatrix()” but this seems to only be able to apply the matrix to the entire geometry rather than the vertices I require. Is there any way to specify which vertices or faces the applymatrix will apply to? Hopefully this makes some sense!!

No. You have to iterate over all vertices and selected the relevant ones. You can then use Vector3.applyMatrix4() in order to transform a single vertex. When iterating over an indexed geometry, you have to watch out to apply the matrix transformation only once to the respective vertices.