Low Water Pressure Due to Dirt from Well Water?

Due to the recent storm and heavy rain, our well got disturbed and that caused heavy sediments and dirt in the water. Our whole house water filter got heavily clogged, and let the dirt pass through all the pipes and messed up the plumbing.

We managed to clean the toilet tanks by taking out all the dirt, one of our shower still has very low pressure. The sink right next to it works fine. We are not sure how to clean the dirt that is already inside the pipes. Any tip is appreciated. :-)

By Sam