We give a $C^1$-perturbation technique for ejecting an a priori given finite set of periodic points preserving a given finite set of homo/hetero-clinic intersections from a chain recurrence class of a periodic point. The technique is first stated under a simpler setting called Markov iterated function system, a two dimensional iterated function system in which the compositions are chosen in Markovian way. Then we apply the result to the setting of three dimensional partially hyperbolic diffeomorphisms.