The work done is zero when the force is acting perpendicular to the fsurface .this is becacuse cos90 is =0 .My question is why are we taking cos 90 here.

In this case the work done is the dot product force and distance,
F·ds = Fcosθds
where θ is the angle between the force vector and the direction of movement
In the notable case of a force applied to a body always at an angle of 90 degrees from the velocity vector (as when a body moves in a circle under a central force), no work is done at all, since the cosine of 90 degrees is zero.

Approved