it all depends on what your trying to achive! what are you trying to do?
If I get you right you want to break the inheritance from the top level site so that it doesnt effect any other sub-sites?
Aslong as you dont change the toplevel masterpage that all the sites and subsites sit on then you can change as you please ;). If you change a subsite then it should only change any sites below it only! I dont think the parent can inherit the masterpage it only goes down not up!
So If your site is in a site collection you can change the masterpage and it will only effect that site and anything below it!
go to the homepage of the site you want to change and click on siteactions sitesettings then:
Once you have done the above you can:
You can select the masterpage you want for that site and click on:
Apply to this site
Apply to this site and all its subsites
Hope this helps :)