convert 2d to 3d

 I need to convert thousands of 2d sdf file to 3d mol2 files and add
 charges. But I met a problem. Concord and Corina is too expensive. Concord
 is built in the alchemy2000 that is not very expensive. I have a
 question before I buy Alchemy2000. Can I run  Alchemy2000 in batch mode? I
 mean, can I use alchemy2000 to convert thousands of 2d file to 3d
 Thank you in advance.
 jianquan chen