pepillo,
employers will first scan your resume/CV for past and present work experience and skill sets.
if you have experience in the kind of MCUs they hope to use or are using, they will pick you for an interview.
if not, they will still see if you have worked with other MCUs and development tools.
they will also look at the kind of real industrial projects such as a mobile phone, PDA, GSM base station, switch box, bluetooth MP3 player for examples, which you have done using this MCUs.
Most universities only teach one or at most two MCUs.
Personally I was taught MC68HC11. I learnt PIC18F452, Intel8051, Zilog Z8, ARM7/9/11 and OMAP, MIPS, Atmel128/8 etc on my own when I worked with them.
You have to learn many things on your own. Degree gives you the foundation. After you graduated, you are on your own to explore, with this basics knowledge in your head.
lastly they will still check for your "sheepskins". in other words, they want to see your qualifications such as MSEE or BSEE.
You dont need a MSEE to become a MCU or an embedded system engineer. BSEE is good enough.
Look at it this way. Many engineers from "unheard" and village universities in India or China with BSEEs found jobs as engineers working with MCUs in the USA.
Do you think they care so much about needing MSEE?
So long you are technically good and experienced, even a degree from India and China still get you a decent employment as far as USA.
I need to stress this. Not having a BSEE is really a disadvantage because you are less competitive compared to cheaper labour from India and China where BSEE is nothing at all and everyone has one.