How do I get the handles of all open figures in MATLAB

There are a few ways to do this. One way to do this is to get all the children of the root object (represented in prior versions by the handle 0):

figHandles = get(groot, 'Children');  % Since version R2014b
figHandles = get(0, 'Children');      % Earlier versions

Or you could use the function findobj:

figHandles = findobj('Type', 'figure');

If any of the figures have hidden handles, you can instead use the function findall:

figHandles = findall(groot, 'Type', 'figure');  % Since version R2014b
figHandles = findall(0, 'Type', 'figure');      % Earlier versions