Remove the skin and seed. Here is a prep chart that can help answer any additional questions! http://www.nutriliving.com/infographics/extraction-prep-chart
I had a look at the prep chart. I personally eat the skin and seeds of organic apples (the only kind to buy!) and do not peel anything unless the skin is blemished or shriveled, etc. To remove pesticides, rinse in Structured Water, which will neutralize all toxins energetically. To understand how this works go to www.thewellnessenterprise.com and read "Scientific Minds Want to know." Structuring my water has transformed my health and life.