No, they are not removed when you select standard deduction on the federal return. The medical expenses are ignored on your federal return if you are using the standard deduction. But they are still available to use on your state return if your state allows using a different deduction. Some states allow you to change, some don't. The expenses are entered on your federal return and transferred to your state return(s). If your medical deduction was not included on your NJ, you can amend to add the deduction.
NJ doesn't have a standard deduction or itemize deductions. New Jersey law provides several gross income tax deductions that can be taken on the New Jersey Income Tax return. New Jersey does not allow federal deductions, such as mortgage interest, employee business expenses, and IRA and Keogh Plan contributions.
On your NJ return, you can deduct from your gross income certain medical expenses that you paid during the year for yourself, your spouse or domestic partner, and your dependents. However, you cannot deduct expenses for which you were reimbursed. Only expenses that exceed 2% of your income can be deducted. See NJ Exemptions & Deductions
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