An application for amnesty must be filed with the INS within 90 days of the bill passing. Not coming forward and filing within the period allowed will be an automatic felony. No court time needed. You’re here and you didn’t file, so you’re guilty.
Bill of attainder. Violation of Article I, Section 9, U.S. Constitution.
http://www.techlawjournal.com/glossary/legal/attainder.htm
Since they would have 90 days (considering the mess at the State Department with passports - I'd extend that to one year) AFTER the passage of the bill to apply for amnesty, that would not be an ex post facto law.
As for the bill of attainder problem, we would still require court trials, but the person's mere presence within the borders of the United States would be considered prima facie evidence of guilt.