The best practice is to build a repeatable process for creating your AMIs from a base operating system image (typically AWS Linux, Ubuntu, etc.). The reason is that you have many more updates ahead of you:
- You might not succeed at fixing the identified issues completely to Amazon's satisfaction
- Future scans may find new, different issues
- AWS Marketplace staff will manually check some things with your AMI
- You might find your own bugs
- You will eventually want to deploy new software versions
Yes, you could launch an instance from your your image, modify it, save it, and make a new image. It might be worth doing that to learn something about the AMI scanning criteria.
But you would not make any progress towards a reliable, repeatable image building flow. I strongly recommend looking into tools like Packer that can help you automate the AMI building process.