You cannot modify a file once it is in HDFS, except by appending to it. See this answer that confirms that append is possible:
Append data to existing file in HDFS Java
Map reduce allows you to operate on a file in parallel, with each mapper reading a block of the file, and many mappers running at once. This is how it is designed to work.
Any given mapper could filter rows and write out all, some or none of them to a new file pretty easily.
If you use map-reduce to write out the modified file, by default it will appear as a directory of files which can be combined into a single file depending on your requirement.