Currently, fruit removal using multi-directional canopy and trunk shakers are the most widely used technique for harvesting nut trees. To develop an intelligent harvesting machine, a system needs to be developed to shake each tree optimally. Optimum mechanical harvesting machines aim to maximize fruit removal with minimum tree and fruit damage, using the least amount of energy. Maximum fruit removal requires the tree to be shaken around its natural frequency; however, the best shaking frequency is not the same for all trees. The natural frequency of a tree is a function of its morphology, size, mass, branch configurations, wood properties, and density of leaves. The natural frequency could also change during harvest. For instance, when a tree is shaken and fruit drops, the natural frequency shifts due to changes in the mass.In this work, vibration transmission in trees is studied to enhance mechanical harvesting machines while minimizing damage to the tree. Trunk shakers and canopy shakers are the most common commercial mass harvesting machines, each comes with a limitation. Further, a trunk shaker has more energy loss from tree trunk to its canopy compared to a canopy shaker. The efficiency of the commercial harvesting machines is evaluated by quantifying the energy input to the trunk and the transferred kinetic energy throughout the tree canopy. A set of wireless accelerometer sensor systems was developed and used to measure acceleration at different parts of the tree and the shaker machines. A mathematical model of vibration and force transmission throughout a pistachio tree is developed under different shaking conditions using a trunk shaker. A new method was developed to find proper shaking intensity as a function of the tree trunk size. Two canopy shakers were designed, fabricated and tested in the field for harvesting table olive trees. One design included an adjustable head, and one included a large canopy shaker for larger mature trees. It was found that a combination of canopy and trunk shaker results in the highest harvesting efficiency in olive trees. Chapter one is mainly a review of literature of different types of mechanical harvesting methods. Chapters two and three are focused on mathematical modeling of variation and force throughout a pistachio tree while shaking using a trunk shaker. Chapters four and six presents two new canopy shakers specifically designed for table olive harvesting. The effectiveness of using two shaker machines at the same time is discussed and evaluated in Chapter five.