In 1994 he received the Lucia R. Briggs distinguished Alumni Award from Lawrence University and in 2000 he was named Entrepreneur of the Year for Emerging Companies by the Silicon Valley Business Journal.  He has been elected to the status of Fellow in two international scientific societies, the American Association for the Advancement of Science and The Optical Society of America (OSA), and served as the president of OSA in 2009. In 2017 Baer was elected a Corresponding Fellow of the Royal Society of Edinburgh (CorrFRSE).
He is a visiting professor at the University of Strathclyde in Glasgow, Scotland.
Baer received an honorary doctorate from Heriot-Watt University in 2012 
In 2012, he was also awarded the Robert E. Hopkins Leadership Award by the Optical Society (OSA).