| I suggest you contact your CPA or Tax adviser who will either file all the delinquent payroll quarterly tax returns or he would suggest a Payroll company to assist you in meeting full compliance with respect to your payroll tax returns.
The penalties for delinquent payroll tax return filings is 10% of the total tax liabilities, and in addition, you would also be assessed statutory interest as well on all outstanding tax liabilities. I suggest that you avoid the 1099-Misc filing option as it appears that the employee was really a full time employee | 
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