Today the CAHSRA Supplemental Alternatives Analysis Report was published. It carries forward two alternatives for further consideration in North Central and downtown San Mateo:
Option A — an aerial viaduct (kind of like a freeway structure), or
Option B — an open trench that would pass below street intersections
The option of a tunnel or covered trench has been eliminated from consideration. If you click on the High Speed Rail tab above you will find links to the full Supplemental Alternatives Analysis Report and the Executive Summary.
Once CAHSRA settles this issue of “vertical alignment”, whether the trains will run up in the air or down in a trench, they will take on the “horizontal alignment” or where exactly the the trains will run in the sense of east or west.
North Central Neighborhood 
As per a recent article (August 8th)I found on the Burlingame Voice website the following has been confirmed per this article:
“In the Federal Funding Application submitted on Friday, August 6th, the Authority requested the following:
“New infrastructure providing four tracks between Brisbane and Redwood junctions is proposed based on the more economical Aerial Structure cross-section as opposed to the Trench solution in some areas such as Burlingame, San Mateo which would be more expensive (see figure 2).”
Page 4 of the ARRA application confirms this. Refer to the Burlingame Voice website for further information and personal comments.