Please ignore

$$\begin{align}
\in(12) = &6
\in(&6) = &4
\in(&4) = 3
\end{align}$$

Question

Please ignore

$$\begin{align}
  \in(12) = &6
        \in(&6) = &4
              \in(&4) = 3
\end{align}$$

anonymous · Answer

$$
  \in(\color{#ff00ff}{12}) = \color{red}{6} \
  ~~~~~~~~~\in(\color{red}{6}) = \color{blue}{4} \
  ~~~~~~~~~~~~~~~~~\in(\color{blue}{4}) = \color{green}{3}
$$So, $\in(\in(\in(\color{#ff00ff}{12})))=\color{green}{3}$.

e.mccormick · Answer

You could use a matrix or array to align it.
$$\begin{matrix}
\in ({\color{Magenta} {12}})=& {\color{Red} 6}& & \ 
  & \in(\color{Red} 6) & = {\color{Blue} 4} & \ 
 & & \in (\color{Blue}4) & = {\color{DarkGreen} 3}
\end{matrix}
\
\begin{array}{rrrr}
\in ({\color{Magenta} {12}})&= \color{Red} 6& & \ 
  & \in({\color{Red} 6}) & = \color{Blue}4 & \ 
 & & \in (\color{Blue}4) & = {\color{DarkGreen} 3}
\end{array}$$

Also, for long spaces there is \quad and \qquad
a\quad  b \qquad c$\rightarrow a\quad  b \qquad c$