Q:

Pressure being isotropic

We say pressure is isotropic.  At any point in a fluid pressure acts equally in all directions, but pressure is perpendicular force per unit area so how can pressure be there in all directions as pressure will only exist if fluid molecules apply force perpendicular on other molecules. 

A:

Fluid molecules apply force perpendicular on other molecules. 

This does happen. 
But because many molecules surround a single molecule, the net force cancels out and so there is net effect of this force.