How do you get rid of all bubbles in clean water?

There are several options depending on the desired result.

If one merely wants to remove bubbles, but does not care if one removes all dissolved gasses causing the bubbles, one can just wait and bubbles will float to the top and disappear though agitating the vessel to dislodge them from the sides may be required.

A more effective way to remove gas bubbles from water is to subject it to reduced pressure. One could place the liquid into a partial vacuum, but too high a vacuum and the water will start to vaporize and evaporate and can even boil vigorously.

Heating can help. Warm water has less ability to sustain dissolved gases than does cold water, hence warm water will more readily release the dissolved gases.

Finally, distilled water has much much less dissolved gas and does not readily form bubbles.

As an aside, if the water is not clean, bubbles are more readily formed and more resistant to removal. The tendency to form bubbles is, in fact, a crude way to assess purity of water.

Some of the less logical ways are using a vacuum or a needle and poke it