you can try using findall(0) -- root matlab handle, then looping over all the handles to find the right handle. What I wanted to do in my application is to search for an open Signal Builder window so I did this:
hndls = findall(0);
Tags = arrayfun(@(x)get(x, 'Tag'), hndls, 'UniformOutput', 0);
sigbuilderwin = hndls(strcmp(Tags, 'SignalBuilderGUI'));
Hope this helps
