Because it is a text file, you will need to read the text file, and create a new text file that has only the contents you want to keep: the parts you want to remove should just not be written to the new text file.
None of MS Windows, OS-X or Linux (the operating systems that MATLAB is supported on) have any mechanism to delete something out of the middle of a file. The operating systems themselves do all provide ways to truncate a file at a given point, removing everything from there to the end of the file, but MATLAB does not provide access to that operating system facility. The only way in MATLAB is to copy what is still wanted and not copy what is no longer wanted.
