A major concern with mixing modern multiuser OSes and cryptographic code is that at any time the code (including secret keys) could be swapped to disk, where it can later be read by an attacker, or left floating around in memory for later retreval.
For this reason the library uses a std::vector with a custom allocator that will zero memory before deallocation, named via typedef as secure_vector. Because it is simply a STL vector with a custom allocator, it has an identical API to the std::vector you know and love.
Some operating systems offer the ability to lock memory into RAM, preventing swapping from occuring. Typically this operation is restricted to privledged users (root or admin), however some OSes including Linux and FreeBSD allow normal users to lock a small amount of memory. On these systems, allocations first attempt to allocate out of this small locked pool, and then if that fails will fall back to normal heap allocations.
The secure_vector template is only meant for primitive data types (bytes or ints): if you want a container of higher level Botan objects, you can just use a std::vector, since these objects know how to clear themselves when they are destroyed. You cannot, however, have a std::vector (or any other container) of Pipe objects or filters, because these types have pointers to other filters, and implementing copy constructors for these types would be both hard and quite expensive (vectors of pointers to such objects is fine, though).