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typedef std::stack<Eigen::Affine3f> MatrixStack;
MatrixStack m_transformation_stack;

Eigen::Affine3f m_transformation;

..//did something to m_transformation;

m_transformation_stack.push(m_transformation);


My code breaks at the last line when I am pushing a matrix into the stack.

Also, it only breaks in release mode, not debug mode, I am using vs2010

The exact error message is:
Microsoft Visual Studio C Runtime Library has detected a fatal error in Millipede2012_version2.exe

Any one have any idea?

probably an alignment issue. You should use our aligned allocator:
std::stack<Eigen::Affine3f, Eigne::aligned_allocator<Eigen::Affine3f> >

or use non-aligned Affine3f:

typedef Eigen::Transform<float,3,Eigen::Affine, Eigen::DontAlign> UnalignedAffine3f;

std::stack does not build for me on VS2012 with specified allocator, therefore a solution is to simply use std::vector push_back, pop_back, back()...