A federal judge has rejected claims by ex-employees of Bernard L. Madoff that the government is interfering with their right to defend themselves by belatedly treating money set aside for attorney’s fees as forfeitable assets.

Southern District Judge Laura Taylor Swain refused to dismiss the indictments against Daniel Bonventre, Annette Bongiorno and Joann Crupi, former employees of Bernard L. Madoff Investment Securities who were charged last year with securities fraud conspiracy, falsifying records and a host of other crimes as part of Mr. Madoff’s unprecedented Ponzi scheme.