Is possible to use manual refuel in Kerbal Space Program?

To transfer fuel you will have to dock your vessels. This can be done either using docking ports on both vessels or a "grabbing unit" aka the "claw" on one of them. You will also need to have at least one upgrade of the science facility back at the Kerbal Space Center to enable resource transfer.

Once your vessels are docked, right click the source and the destination tanks while holding Alt, and use the In/Out buttons to transfer fuel as needed.

If docking the two vessels is impractical, you can use a small rover or spaceship to move the fuel.

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Regarding the yellow pipe, it can only link parts on the same vessel, so you cannot use it to transfer fuel between vessels. But with resource transfer, if the tanks are part of the same vessel, then the pipe is not needed. It's purpose is really only to allow engines to draw fuel from tanks from which they would not draw otherwise.

However if you would rather use a pipe to transfer fuel, and you are playing with mods, the Kerbal Attachment System mod does offer pipes to do this.