Well, evidently the processors worked with binary instructions, but these were based on primitive Lisp operations. There's more information in http://hdl.handle.net/1721.1/5731 and quoting from the wikipedia http://en.wikipedia.org/wiki/Lisp_machine

  These machines had hardware support for various primitive
  Lisp operations (data type testing, CDR coding) and also
  hardware support for incremental garbage collection. They
  ran large Lisp programs very efficiently.