Hire an attorney to make your argument. If it is determined that what you have planted are weeds, then you will be ordered to cut them down. Or you can cut them down prior to court. You don't have a lot of options.
You need evidence that the "native species" you planted are such, and are landscaping rather than weeds. You need to read the relevant ordinance and see if there are definitions. You probably will need a landscape architect or nurseryman to provide evidence that your plantings are not weeds. I would also look to see if the local agricultural extension has any information on native plantings, low maintenance yards or "xeriscaping" that would support your claim that the yard is planted rather than overgrown.
I also would try talking to the local zoning/code enforcement people about the issue. If you have documents or other backup to support your claim that these are plantings, provide it to them. Also ask them exactly what they want you to do.
Finally, if you can't resolve it, strongly consider bringing an attorney to the code enforcement hearing. Don't rely on comments or information on this board, from friends, or other friendly advice to protect your rights. If you are found in violation, the fines and issues with correcting the problem can be signficant.