Studying high-dimensional Hamiltonian systems with microstructure, it is an important and challenging problem to identify reduced macroscopic models that describe some effective dynamics on large spatial and temporal scales. This paper concerns the question how reasonable macroscopic Lagrangian and Hamiltonian structures can by derived from the microscopic system. In the first part we develop a general approach to this problem by considering non-canonical Hamiltonian structures on the tangent bundle. This approach can be applied to all Hamiltonian lattices (or Hamiltonian PDEs) and involves three building blocks: (i) the embedding of the microscopic system, (ii) an invertible two-scale transformation that encodes the underlying scaling of space and time, (iii) an elementary model reduction that is based on a Principle of Consistent Expansions. In the second part we exemplify the reduction approach and derive various reduced PDE models for the atomic chain. The reduced equations are either related to long wave-length motion or describe the macroscopic modulation of an oscillatory microstructure.