Alright so the title says it all.
I am working on a method called Separation of Variables with differential equations. The original problem was Y'= cos^2y.
I am wondering since I was trying to get "Y" all alone and move the tangent to the other side if that was acceptable or is there no way of doing it?
You appear to have divided each side by $\tan(x)$. Sadly, this isn't valid, for a couple of reasons:
Less importantly, for some $x$, $\tan(x)=0$: this would amount to division by zero.
You didn't include the argument of the tangent functions, i.e. the $(x)$ bit. This is important to be sure what your variables are.
More importantly, you seem to have thought that
$$\tan(y)/\tan(y) = Y$$
The latter is wrong, because dividing something by itself should give you $1$.
So what should you do?
My recommendation: take the arctangent of both sides; it is the inverse function of tangent. Thus,
$$\arctan(\tan(y)) = y$$
Then, doing this, you'd get
$$y = \arctan(x+C)$$