Indirect evidence must be used to study the structure of atoms, because the direct evidence affects the position and energy of the particles of the atomic structure.
For example, imagine you use a light ray to find the location of an electron in an atomic structure, the current location of the electron you are now seeing is as a result of the light ray, and the electron has changed it's initial position to a new position as a result of the effect of the light ray.
So indirect means would probably give more accurate answers about the atomic structure than that of the direct means.
An example of the indirect means would be for example setting up a mathematical equation or model of the atomic structure and trying to provide solution for the model or equation.
