If the html files you are working with are well formed (xhtml) then you can also use XML libraries in java to find particular tags and modify them. The IO itself should be handled by the particular libraries you are using.
If you choose to manually parse the strings you could use regular expressions to find particular tags and use the java io libraries to write to the files and create new html documents. But this method reinvents the wheel so to speak because you have to manage tag opening and closing and all of those things are handled by pre-existing libraries.
Look at http://java-source.net/open-source/html-parsers for a list of java libraries that parse html files into java objects that can be manipulated.