What is the best technique I can use to encrypt inner nodes in B+tree? I'am working on searchable encryption.

First I create an index for a set of files. The index is B+ tree. The leaf of this tree is a bloom filter which represents the words in each file. Each bloom filter represents one file. Inner nodes represent XOR of these leaf nodes.

Last but not least: to encrypt this tree, I'ld like to encrypt each leaf node separately, but I'm confused which techniqe should be used to encrypt the inner nodes – while keeping it easy to do searches in this tree. What is the best technique I can use to encrypt inner nodes in B+tree?
We don't know your scheme, so we cannot say which technique is better for you, but in most earlier schemes that use binary vector (or any integer vector) for store information, Secure Inner Product is most used tools for encrypting! And it's useful for searching in some condition and depend on search construction.

P.S. Why you using bloom filter that has false positive issue?
I'm working on SE too.