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Topological insulators are distinguished from normal insulators by their bulk insulating gap and odd number of surface states connecting the inverted conduction and valence bands and showing Dirac cones at the time-reversal invariant points in the Brillouin zone. Bi-based three-dimensional strong topological insulator materials, Bi$_2$Se$_3$ and Bi$_2$Te$_2$, are known as high temperature topological insulators for their relatively large bulk gap and have one simple Dirac cone at the $\Gamma$ point. In spite of their clear surface state Dirac cone features, the Dirac point known as a Kramers point and the topological transport regime is located below the bulk valence band maximum. As a result of a non-isolated Dirac point, the topological transport regime can not be acquired and there possibly exist scattering channels between surface and bulk states as well. In this article we show that an ideal and isolated Dirac cone is realized in a slab geometry made of Bi$_2$Se$_3$ with appropriate substitutions of surface Se atoms. In addition to Dirac cone engineering by surface atom substitutions, we also investigate Bi$_2$Se$_3$ thin films in terms of thickness and magnetic substitutions, which can be linked to applications of spintronics devices., Comment: 4 figures