Problem with stick shift, Nissan sentra GXE 2000 manual.?

It could be the linkage, but more than likely, the clutch isn't fully disengaging. Are you sure that you are pushing the clutch pedal all the way to the floor before you shift? If so, the problem could be anything ranging from a bad throw-out bearing to a bad clutch master or slave cylinder. You need to take it to a mechanic for a diagnosis before it wears out your clutch and/or flywheel.