We have developed a research compiler for Java class files. The compiler, which we call Briki, is designed to test new compilation techniques. We focus on optimizations which are only possible or much easier to perform on a high-level intermediate representation. We have designed such a representation, JavaIR, and have written a front-end which recovers high-level structure from the information from the class file. Some of the high-level optimizations can be performed by the Java compiler which produces the class file. There is however a set of machine-dependent optimizations which have to be customized for the specific architecture and so can only be performed when the machine code is generated from the bytecodes, e.g., in a Just-In-Time (JIT) compiler. We choose memory hierarchy optimizations as an example of machine-dependent techniques. We show that there is an intersection of the set of machine-dependent optimizations and the set of high-level optimizations. One such example is array remapping which requires multi-dimensional array references which are not present in the bytecodes and at the same time requires information about memory organization. We develop a set of optimizations for accessing array elements and object fields and show their impact on set of benchmarks which we run on two machines with a JIT compiler. The execution times are reduced by as much as 50% and we argue that the improvement could be even higher with a more mature JIT technology.