There is a special program for this - the Delinquent Informational Return Program. Examples of informational returns are 5471 (foreign corporation), 3520-A (foreign trust)
Participating in this program would entail 3 amended returns for each of the past 3 years (assuming you have not filed the informational return for all three years), and forms 5471 (assuming that is the missing form) for each year.  Finally, a reasonable cause statement must be attached.
Potential for filing FATCA (form 8938) if the balance on the company accounts (previously unreported) puts the taxpayer over the threshold