How to set upper bounds with "greater than(>)" type instead of "greater than or equal to(>=)" for fmincon?

I have a 4D matrix of variables in my nonlinear model. Not all variables are valid in my model depending on the example. There was no way for me to make a less complicate matrix of variables since I need to cover different levels of a factory(each level has a dimension) and I want my model to be in general form to be able to cover models that include full number of variables(the whole 4D matrix)

I tried setting zero for some elements of the 'ub' but in Matlab ub is greater than(>) the x values and not greater than or equal to(>=) them. that forces me to set a very small value(for example 0.000000001) for the upper bounds of the invalid variables. but that doesn't stop Matlab from changing the values of those variables and that means I do not get an optimum and feasible solution for my actual model.

Thanks in advance.