Total Commander

Sometimes I need to replace the "." in filename, but the multi rename tool will replace the "." before the extension too, and I can't find any method to avoid it.

So I'd like to have the option to limit the range where the Search/Replace will be take effect, like " in Filename only" "in extension only".

You may use following trick to get what you want:
So first replace loop will remove dots (or replace, if you type something before pipe in 'replace with' field), and second replace loop will replace strange string _$_dot_$_ with dot - but this string presents only before extension so it will recover lost dot between file name and extension. (if you replace dot with something non-empty string, just insert it before _$_dot_$_ both in extension and in replace with so replacer will remove it)

If you don't know about multiple replace operations during single rename operation, press F1 in rename tool window:

New: You can now search+replace multiple strings in one step! The strings need to be separated by the vertical line (Alt+124).