Found solution:

I needed transform.worldToLocalMatrix to transform

world coordinates to local mesh coordinates. this whole script:

var mesh : Mesh;
var vertices : Vector3[];
var Mypos:Vector3;
var Mypos1:Vector3;
var hit : RaycastHit;
var thisMatrix: Matrix4x4;
var meshMatrix:Matrix4x4;


function Start(){
    thisMatrix = transform.localToWorldMatrix;
    meshMatrix = transform.worldToLocalMatrix;

    mesh= GetComponent(MeshFilter).mesh;
    vertices = mesh.vertices;

}

function Update(){


    for (var i = 0; i < vertices.Length; i++){

       Mypos = thisMatrix.MultiplyPoint3x4(vertices[i]);
       Mypos.y+=100;

       if (Physics.Raycast (Mypos, -Vector3.up,hit, 120)) {
       Mypos = meshMatrix.MultiplyPoint3x4(hit.point;);
       vertices[i] = Mypos;        
       }

    }
       mesh.vertices = vertices;
       mesh.RecalculateBounds();
}