Yes, when booking the Trail, indicate that you want to sleep alone. There is an additional cost of €45 per person for bringing an extra tent.
On the Lares and Salkantay Trails, you will spend the last night in a hostel. By default, you share this room with someone from your group. It is possible to reserve a private room for an additional cost of €20 per person. Please inquire about this when making your booking.