You can do this by exporting your transfer function from the Control System Designer to the MATLAB workspace and then plotting the root-locus in MATLAB.
As an example, you can run the commands
h = tf([2 5 1], [1 2 3]);
rltool(h);
and then select Export, select LoopTransfer_C, and hit the Export button. LoopTransfer_C is now in the MATLAB workspace. Now use
rlocus(LoopTransfer_C)
to recreate the root-locus figure.
