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I am designing a small DAC and I want to clean the power supply (it's noisy). I used a PI filter.

However, after the PI filter, I need an electrolytic capacitor (330 µF) to help with some transients. The problem is that the output of PI filter has a capacitor that is in direct correlation with the L...so by adding this electro capacitor I will change that correlation. Any pointers on what to do?

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The extra capacitance will obviously change the characteristics (i.e., frequency response) of your Pi filter, but the key is, it won't make it worse for your application in any way. Go ahead and hook it up.

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