First of all I list all the rules including line numbers like this;
iptables -L -t nat –line-numbers
I then look at the output that will be similar to the below
In this example lets say I want to delete rule number 2 in the PREROUTING chain, I would enter the following;
iptables -t nat -D PREROUTING 2
In English the above line means remove line number 2 from the PREOUTING chain, I would then run the first command again to check my iptables file, then save the iptables file and restart the iptables service.
iptables -L -t nat –line-numbers
service iptables save
service iptables restart
All the above is carried out running on Centos, you may have to edit slightly for your particular distribution.