I searched the Haut-Rhin archives website for their index to "fonds" (not sure what the English word would be...bins, boxes?) and there is a series Y of records that relate to prisons. Here is the index record for series Y:http://www.archives.haut-rhin.fr/resource_context/a011443776...
This PDF file is an index to Series Y (prisons) at the Haut-Rhin archives:http://www.archives.haut-rhin.fr/medias/customer_2/Archives_...
It is 28 pages long with lots of listings and would probably take a couple hours to go through to determine what would be good fonds to search.
The index record for the Y series also has a page with relations to other series:http://www.archives.haut-rhin.fr/resource/a011443776144eDIcx...
Of the listings on that page, here are ones that may be relevant to you:
4 M 264-272 : prisonniers politiques (political prisoners)
In these next two, the second character is the letter 'o', not the number zero:
2 0 (dossiers dans l'ordre alphabétique des communes) : maisons de transfèrement et prisons municipales (not sure what a "maison de transferement" is [center for transfers?]; town jail)
2 0 407 et 409 : maison d'arrêt, de justice et de correction de Colmar (maison d'arret is a short-term holding jail, like a county jail in the US; maison de correction is a youth detention facility; and maison de justice provides many legal services provided by the government, so akin to a county courthouse in the US)
Series U: arrêts et jugements des cours et tribunaux (orders and judgments of the courts and tribunals)
3 Z 28 : prisons de l'arrondissement de Colmar (prisons of the Colmar arrondissement)
As you can probably figure out, unfortunately, it would take a long time to search the records at the archives in Colmar.