For the formula to work, the conductor must be a cylinder. That is, its cross section must be the same at all points along its length.

Then the cross-sectional area is the same no matter which location along the length you choose to measure it at. 

The cross sectional area is simply the actual cross-sectional area, regardless of how complex the shape of the cross-section is.

Of course if you were to talk about things like fractal shapes, with microscopic features, this model might break down if the features of the shape approach the size of the material's molecules (or even of the crystal grains, which are much bigger than single molecules).

> How can i calculate its length and area of cross-section after taking any two point om its surface as end points.

For the formula to apply, you must apply the end voltages uniformly across the two end surfaces of the cylinder. You can't apply it at single points. However, the error from doing so will be very small if the length of the cylinder is much greater than the diameter of the cross-section.

If the conductor is not a proper cylinder, you'd have to find its resistance by a numerical calculation. You could either approximate its shape as a sequence of shorter cylinders, or you could do a full 3D finite element model of the whole shape.