I am an Australian citizen who married a US citizen sept 7th 1997 when i was legally here on a visa.
My conditional residence expired on 02/22/2001 and i filed form 1-751 but with the wrong fee. It was stamped as received but sent back without being filed. Due to circumstances, i never refiled.
It is now 3 yrs overdue with filing, and i have been seperated, although not divorced from marriage for the past 3 yrs.
I don't know what to do. I can't afford an expensive lawyer and am scared of refiling if i will get sent out of the country. Do i have any rights?

You really need to speak to an immigration attorney. You currently have no legal status and will have to be placed in removal proceedings (i.e., deportation proceedings before an immigration judge) in order to sort things out.

If you are unable to afford a private attorney, there are non-profit legal organizations that provide legal assistance to low-income individuals. You can find a list of such organizations in your area by consulting the web site for the immigration courts at

http://www.usdoj.gov/eoir/probono/states.htm