the owner of my company gave me a loan to buy a car after mine was totalled.
can they hold my final check since i still owe on the loan

Part of the difficulty in answering your question is you don't say
what state you live in. Most applicable laws vary by state. And in
many cases, employers cannot withhold salary (except federal/state
taxes) without written consent from the employee. In that case, you
will want to look at your loan agreement to find out what actions the
employer can take if you default on the loan.

Assuming you have not defaulted on the loan, it's unlikely they will
even attempt to withhold your last check. However, if they improperly
attempt to withhold your check, you should immediately contact your
state department of labor. The various state addresses can be found
here: http://www.dol.gov/esa/contacts/state_of.htm

More discussion on this issue can be found here:
http://www.entrepreneur.com/article/0,4621,297435,00.html

It is unlawful for an employer to withhold wages for items other than
mandatory taxes in nearly every locale, EXCEPT when you have given the
employer WRITTEN permission to do so.

If you post your location, this can ve verified easily at the "labor
standards" section of your states web site, specifically the section
on "separation of employment" and "final paycheck."