First be sure your body, hands are clean and start with positive mind frame.
Be sure that the Yantra is placed such that you would be facing east while worshiping it.
Light a diya or jyoti in front of Gayatri Yantra.
If it is possible then put some (2-3) fresh flowers in front of Yantra.Chant the Beej Mantra provided with the Yantra 108 times. If you are unable to read Sanskrit read Hindi or English Translation, all have equal effect.
Now conclude your worship by sincerely asking the Yantra, in spoken words, to grant you whatever your heart desire.