This is something you should discuss with the lawyer who successfully defended you at trial as s/he would be in the best position to give you advice.
Assuming that you are not a high priority target of multiple law enforcement authorities (think Al Capone), or the evidence is not needed/wanted for prosecution of others, it all depends on the nature of the evidence, who was handling the prosecution, whether state charges are a possibility (if the prosecution was in federal court) of federal charges are possible (if the prosecution was in state court). Normally after an acquittal evidence is eventually discarded or if requested, made available for return to the person from whom it was obtained, if that person wants it.