"Editing" atom nucleus
In part, your vision already exists and uses electrons as "ink". In a process kown as electron capture, a proton "swallows" an electron of sufficient energy and is thus converted to a neutron. 

$$\ce{^{A}_{Z}X + e- -&gt; ^{A}_{Z-1}Y + \nu_{e}}$$

As a consequence, the atomic mass number A remains the same, but the atomic number Z is decreased by one: Element X is converted to element Y.

A typical example would be the conversion of aluminium to magnesium:

$$\ce{^{26}_{13}Al + e- -&gt; ^{26}_{12}Mg + \nu_{e}}$$