Hi Andy,
By wiring the output of a waveform directly into the Write File.vi, the format will by default by binary. You can extract out each piece of the waveform using Get Waveform Components.vi and then writing each of those components into the file in binary format. However, you will need to find out the format of the binary file that Matlab is expecting.
I have attached a simple VI to demonstrate what I have suggested above.
Thanks and best of luck!
Kileen C.
Applications Engineer
National Instruments