Start NPherno, click Import Objects, upon opening the file, NPherno gives you a choice of objects to import that are part of the md3. Select them all. Click on Ok.
At that point you have the model in the viewing area. On the top right, select All, then click on Object: All. At the bottom, at Frames, click All. At that point, everything is selected for export.
To be on the safe side, you might wanna click on Rebuild Normals and/or Error check Objects…
Click Export Objects, give it a name. Put an internal name. I usually put the same name as the .md3 name. Do NOT click any of the checkboxes. Click Ok.
Put the “new” md3 in a map and it should work.
HTH