Data Mining Methods with Nested Data

I have three general questions that I am really struggling to answer:

a) When we have nested data (e.g. employees nested in departments which are nested in companies which are in specific geographical regions) how data mining methods adjust to nesting?

b) Are data mining methods ""immune"" to nested data because of their goal (i.e. predictive analysis)?

c)Can we use data mining methods (e.g. neural networks, random forests) as precursors of variable selection before we run multilevel analysis?

Please accept my apologies if the general orientations of these questions are inconvenient to you. Thank you VERY much for your help. I am looking forward to receive your wise views.