I'm not sure why you want to make 3D matrix. By connecting all the tables using innerjoin, you can obtain a table which contains all the information you need, like:
table12 = innerjoin(table1,table2,'Keys','date');
table123 = innerjoin(table12,table3,'Keys','ind');
tableOut = table123(:,{'ind','dur','vm','value1','value2','value3'});
If you want to make 3D matrix for some reason, it's a piece of cake!
data3D = cat(3,tableOut{:,{'ind','dur','vm','value1'}},...
tableOut{:,{'ind','dur','vm','value2'}},...
tableOut{:,{'ind','dur','vm','value3'}});
