Question

How were Jews separated from urban populations in Nazi territories?

Answer 1

During what time period? Is the question limited to physical separation?

Answer 2

If you're focusing during the early war years, Jewish ghettos were established throughout Nazi-held areas, primarily in urban centers (like cities). Ghettos were areas physically separated from the rest of the non-Jewish population (most often with walls and gates) and Jews could not leave them. Conditions were often squalid and miserable for everyone within the ghettos.

You can read more on ghettos here:
http://www.ushmm.org/wlc/en/article.php?ModuleId=10005059

Here's a bit more if you want it: Concentration camps were also where Jews and other Nazi undesirables were sent to, but that was often a final destination. When ghettos were being liquidated a few years after the start of war, all inhabitants were deported directly to the concentration camps or exterminated on the spot.

If you're looking at legal separation, the Nuremburg Laws were enacted in the thirties in Nazi Germany depriving Jews of many rights further segregating them from society as a whole. Stores were boycotted and they were made to wear the Star of David on their clothes to identify who they were (if they didn't and they were found out, they would either be arrested or worse).