Highlight an area of my 3D model

You could iterate through the Mesh of the model.. which is stored inside of GameObject->MeshFilter(component)->shareMesh(or mesh).. the Mesh object contains Triangle Indicies, Vertices, Vertex Colors, Normals, Texture Coordinates, etc..

You can definitely change the Color of the Triangle you want to highlight through this Mesh structure contained in the GameObject..

C# Example(not tested, written from mind.. lol)

class TriangleHighlighter : MonoBehaviour
{
    void Start()
    {
        MeshFilter meshFilter = gameObject.GetComponent<MeshFilter>();
        Mesh mesh = meshFilter.sharedMesh;
        Color[] vertexColors = mesh.colors;
        for(int i = 0; i < (int)(vertexColors.Length / 2); ++i)
        {
              vertexColors[i] = Color.blue;
        }
        mesh.colors = vertexColors; // update the vertex colors
    }
}