I believe the the holes you are referring to could be caused by the sapsucker woodpecker.  These birds feed on the sap of trees, hence their name.  They drill holes with their beaks into the tree bark to reach the sugary sap beneath.  Usually, they are only a cosmetic issue on trees.  However, sometimes extensive feeding and the resulting damage can harm the trees.  There aren't any chemicals or sprays available to prevent sapsuckers from visiting your tree(s).  Home remedies such as hanging things that will move in the winds have been said to deter them.  I have included a link to a publication on the sapsucker: http://www.uaex.edu/publications/pdf/FSA-7561.pdf