Of course! The key to any such a design is to understand how ATP works at the nanolevel.

Inside a cell, the free energy stored in the structure of ATP is used to change the configuration of proteins.

The cleavage of ATP to ADP + phosphate gives the transfer of energy a direction. 

The change in protein configuration associated with ATP binding/hydrolysis is then coupled to a system that leads to macroscopic (large scale) movement. 

realistic animations of the ATP-dependent motor proteins myosin and kinesin from the Vale Lab!

Cells use proteins almost exclusively to construct motors because protein molecules are relatively flexible; they can be deformed without the need for excessive amounts of energy. 

At the same time proteins can assemble into complex macromolecular systems that can combine microscopic movements in order to produce large scale movements, such as running, throwing a javelin or pumping blood. 

You will probably want to use proteins of some sort in your machine.  It is possible that other molecules might do, but I do not have any idea of what they would look like -- probably if you figure that out you will become quite famous! 

In any case, the types of movement possible at the microscopic level are really quite limited. 

Changes in molecular shape can lead to contraction, extension or rotation. 

Motor proteins, like the myosins, the kinesins and the dyneins move along cytoskeletal polymers made of actin and tubulin.

The can act as tractors, winches or assemblers/disassemblers.  Winches, assemblers and disassemblers can produce either contraction or extension movements, depending upon the geometry of the system.

Muscle is the most common version of a contractile biological machine.  It uses myosin molecules, assembled into 'bipolar' filaments. 

During muscle contraction, these two filament systems are crawl past one another in a ATP-dependent manner. 

The muscle is 'reset' when an opposing muscle contracts, and pulls the contracted muscle back out to its original configuration.  

Other types of biological motors can be based on polymer assembly/disassembly or contraction/ extension.

An example of this type of system is provided the acrosomal reaction spring used by the sperm of a number of marine animals to attach to the egg.

Another example is the myoneme of various protozoa -- they use this contractile fiber to extend out in search of food and retract back when danger lurks!