Hi Linyang,
First you need to export your surface to your Matlab workspace:
http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Custom_processing
The vertices are in SCS coordinates:
http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface
Then you can convert these SCS coordinates to MNI coordinates:
http://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems
Cheers,
Francois