Technically, the clinic is not your employer, because you have been paid professional fees, and not salaries. So it cannot refund you the amount overwithheld.
That leaves you to collect from the government. There are three options.
1) Tax Refund. That process is a royal pain in the butt. It involves an investigation at the BIR side, and your clinic might be asked to send supplementary documents. The process could take up to a year before you get to see your money.
2) Tax Credit Certiificate (TCC). This option is still indicated in the ITR, but the BIR rarely processes requests for these as there have been scams involving TCCs in the past.
3) Leave the amount to be carried over. This is what I suggest, as the credit does not expire and you can use the credit to settle tax liabilities for future years, during which your income will most likely be more that what you earn today.