I have some points that define an object in 3D space (lets say a pencil) and a vector that tells me the direction the pencil is already pointing to.

I want to know how to make the pencil point to another direction.

so I take a random point of the many that defines the pencil: PencilP =(a,b,c)

the direction the pencil is pointing to: OldD =(x,y,z)

the new direction i want to point to: NewD =(i,j,k)

How do I build the rotation matrix?

Or if there is a faster way to get to the solution I will want to know it too

How i set the new rotation matrix?

"Same way you built the original"

I don't have an original rotation matrix, I only have the points that define the pencil and the vector that define the direction the pencil is already pointing to

I have a collection of points that make a pencil, the pencil is located in the origin and the whole pencil is alredy pointing in a direction that i know and have

now i want to rotate the pencil so the whole pencil points to another direction i give

What do i do?

I have attached some code that will help you do it. I could go into the detail of explaining it. But looking at the code would help you understand it as well. If you have any questions let me know. The code below is how i handle it in my engine

Vector3 lookAtDir = direction;
lookAtDir.Normalize();
float angle = Vector3::Angle(lookAtDir,Vector3::forward);
if(Mathf::Approximately(angle,0.0f))
{
//We are already pointing to the direction.
return;
}
//Compute sin angle
Vector3 axisToRotate = Vector3::Cross(Vector3::forward,lookAtDir);
float length = axisToRotate.magnitude();
if(Mathf::Approximately(length,0.0f))
{
//Direction is parallel.
//Recompute right vector based on new look at direction.
Vector3 newright = Vector3::Cross(Vector3::up,lookAtDir);
axisToRotate = Vector3::Cross(lookAtDir,newright);
}
//Recompute final rotation.
Quaternion to = Quaternion::AngleAxis(angle,axisToRotate);
if(to!=localRotation)
{
localRotation=to;
isDirty=true;
Update();
}

You have your old and new direction vectors, so the problem is simply a matter of building the rotation matrix to rotate the first vector onto the second. You use the cross and dot product to get the rotation axis and angle.

Assuming that oldV and newV are normalised:

axisOfRotation = crossProduct(oldV, newV).normalise(); // Depending on whether your library requires normalised rotation axes

angleOfRotation = arccos(dotProduct(oldV, newV));

Whatever library you're using should have a function that builds a rotation matrix from an axis and angle of rotation, so there's no need to manually code a whole bunch of math.