The only way you could search  the XML file  would be to index it first
and then searching it. You could do this using something like Lucene.
It may be just as fast however to just read through the file from the
beginning to locate the node  in question. 100 MB is really not that big
so it shouldn't take to long to read through it. Now, as for writing it
back out you'll probably want to write to another file, skip the
matching node and write the remainder of the file, then replace the
original file with the new file.