First, install my clean stealth hood templates. There's a link in my signature.
http://modthesims.info/download.php?t=520751
Then go to C:\Program Files (x86)\EA GAMES\The Sims 2\TSData\Res\UserData. There you should see a folder called 'Neighborhoods'. Rename that folder to something else, e.g. NeighborhoodsDisabled.
You have just disabled the first group of townies.
Go to C:\Program Files (x86)\EA GAMES\The Sims 2 University\TSData\Res. There you should see a folder called 'NeighborhoodTemplate' Rename that folder to something else, e.g NeighborhoodTemplateDisabled
You have just disabled the dormies.
Go to C:\Program Files (x86)\EA GAMES\The Sims 2 Nightlife\TSData\Res. There you should see a folder called 'NeighborhoodTemplate' Rename that folder to something else, e.g NeighborhoodTemplateDisabled
You have just disabled the downtownies.
Go to C:\Program Files (x86)\EA GAMES\The Sims 2 Open For Business\TSData\Res. There you should see a folder called 'NeighborhoodTemplate' Rename that folder to something else, e.g NeighborhoodTemplateDisabled
You have just disabled the second group of townies.
Go to C:\Program Files (x86)\EA GAMES\The Sims 2 Bon Voyage\TSData\Res. There you should see a folder called 'NeighborhoodTemplate' Open that folder and take out 'T001' 'A001' and 'M001' but don't take out 'V001'.
You have just disabled the vacation local townies.
Now, you can create your neighborhood and no sims will be added to your neighborhood. You can add your custom university, downtown, shopping district and the three custom vacation destinations and there won't be any sims.
After you have attached the last subhood to your neighborhood, close the game and rename the folders back to their actual name. Now you can open your neighborhood and create your own sims and the neighborhood will only include your sims.