It’s easy to do multiline replace in Notepad++. You have to use \n to represent the newline in your string, and it works for both search and replace strings. You have to make sure to select “Extended” search mode in the bottom left corner of the search window.
I found a good article describing the features here:
http://markantoniou.blogspot.com/2008/06/notepad-how-to-use-regular-expressions.html