We all hate the multi-site blog url that is used. Here is how you can change it or even remove it entirely. Use caution when using this if you have a large network as url structures between posts and sites can become crossed.
To begin you will first go to the permalinks setting for your primary multi-site WordPress website url. Seems confusing? Sorry.
After you are in the permalinks settings make sure default is chosen and that NOTHING else is different. Do not use custom category tags here at all.
Now we need to get back to the network admin area. Open the “All Sites” area and click edit under the primary domain.
Under the settings tab, find permalink setting and change to /%postname%/