As an IC, you decide which benefits you want and which benefits you do not wish to pay for. You chose your retirement plans and their level of funding, your health insurance and its deductible, whether or not you wish to have dental / disability / life insurance and how much you wish to spend on continuing medical education. If you are someone else's employee, these benefits are all chosen for you. If you do not use any of the benefits that your employer provides/selects for you, you do not get the money back, nor do you receive any type of a credit.

If you are an employee and there are employee benefits that you want or need but your employer does not provide you with these benefits, you will typically have to pay the cost of these additional benefits with after tax money, meaning that you must first pay federal, state and Medicare taxes (approximately 41.8% of your pre-tax money in most states at the top of your tax bracket) before you can purchase the benefit.  These "additional" benefits will actually cost you 72% more than if you were able to pay for them with pre-tax dollars, because for every $1.00 you spend, 41.8% would first have to be paid in taxes, leaving you with only 58.2 cents on every dollar to spend on the benefit. Of course, as an independent contractor, you would pay for any appropriate benefits with pre-tax dollars. The same concept also applies to health care expenditures that are not covered by your insurance plan, (deductibles, co-pays, medications or procedures not completely covered by your health care plan, etc.).  Additional health care costs above what is covered by your health care plan are typically not deductible on your federal tax return unless these health care expenditures exceed 7.5% of your gross income.

As someone else's employee, the amount of money that you can save in a pre-tax retirement plan will be decided for you. Many physician employers provide their employees with 401K or modified 401K plans, such that the working physician can put away $30-35,000 per year, or less. As an IC, you can put away far more pre-tax money by utilizing a defined benefit plan, which typically allows you to put away $70-100,000+ per year pre-tax, by the time you reach an age of 35 or so.  As an alternative, you can use a combination profit sharing - 401K plan and can currently put away $48,000 pre-tax per year. Additionally, as an IC, you can incorporate and fund the cash value of life insurance plans, paying tax on only a portion of the money going into the plan, have the money grow post-tax inside the life insurance plan, and concurrently acquire life insurance.  The cash equity of the life insurance plan becomes an after tax asset which then serves to lower your tax bracket in retirement, so that the money in your pre-tax retirement accounts (401K, profit sharing, defined benefit plan, etc.) will go further in retirement.

As an employee, if you are not able to put enough money away in pre-tax retirement plans to meet your retirement goals, you will have to try to save the additional money you need for retirement in after tax savings, on which you will be required to pay any short-term capital gains and/or interest at the top of your current tax bracket (approximately 38.9%, depending on your state of residence), substantially reducing the cumulative gains of these savings.

When comparing IC income to employee income, employers will almost uniformly over estimate the value of the benefits that are being provided by their companies. The easy way to compare how the hourly employee compensation package would compare with that of an IC is to figure out how much each benefit is worth on a yearly basis, then divide by the number of hours you will be working per year to get the hourly value of each benefit, then add the value of that hourly benefit to the hourly employee compensation rate. So, as an example, if an employer provides health care insurance and an equivalent health care plan could be obtained for $600 per month ($7,200 per year), and you plan to work 1800 hours per year, the hourly value of this health care benefit is $4.00 per hour.