terraform plan -target=module.mymodule.aws_instance.myinstance
terraform apply -target=module.mymodule.aws_instance.myinstance
or
terraform plan -target=aws_instance.myinstance
terraform apply -target=aws_instance.myinstance
Disclaimer: Before downvoting the answer, please note that he actually asked to either "exclude" or "run only ec2 resource". And after all this time the exclude feature request is still open in the terraform repo.