Hi,
There are a few options:
1) Rename the files. You could use some sort of quick command-line script like:
> foreach f (wrfout_d01*)
> mv $f $f.d01
> end
This would add a suffix *.d01 to the end of each of the original wrfout_d01 files.
2) Within your WRF running directory (or wherever you have enough space), create a new directory and place all of your original wrfout_d01* files in there:
> mkdir original_d01
> mv wrfout_d01* original_d01
3) Change the name of the "new" wrfout_d01* (actually d02) files by adding something like the following in the &time_control section of the namelist:
history_outname = 'new_wrfout_d<domain>_<date>'
(do not modify the syntax of "d<domain>_<date>". The model expects that exact syntax.
If you would like those to output to a different directory, then try:
history_outname = '/path_where_you_would_like_the_files/wrfout_d<domain>_<date>'
(obviously the path here would be your actual path - not one named "path_where_you_would_like_the_files."