When you fire an alpha particle at a nucleus, the electrostatic forces repel each other, causing it to slow down to a stop before accelerating back in the opposite direction. So the initial kinetic energy is equal to the electrostatic potential energy it has at the point of instantaneous rest, and then you can rearrange the equation to look like this: $$r=\frac{1}{4 \pi \epsilon_0}\frac{Q_{\alpha}Q_n}{E_k}$$ The concept makes intuitive sense to me, you should be able to deduce something about a nucleus' radius by firing positively charged particles at it. But the equation has me confused, can you not just fire the alpha particle with a greater velocity, thus greater kinetic energy, and now your estimation for the radius will be smaller?
So if you choose the velocity at which the alpha particle is released carefully, you could make the estimation equal whatever you want it to equal?