In this paper, we give an efficient method for constructing a large set of disjoint spectra functions without linear structures, which are not equivalent to partially linear functions. This positively answers the open problem [“how to construct a large set of disjoint spectra functions which are not (linearly equivalent to) partially linear functions” raised by Zhang and Xiao]. At the same time, this significantly extends a recent result of Zhang, where a method of specifying four disjoint spectra functions was given. It is demonstrated that such sets can be utilized in the design of highly nonlinear resilient functions. In the second part, based on a generalization of the indirect sum method, we give an alternative approach for designing sets of disjoint spectra functions of even larger cardinality than already given ones, but these functions then admit linear structures. In addition, it is shown that using suitable initial functions in the generalized indirect sum method we can specify highly nonlinear resilient Boolean functions (in odd number of input variables $n$ ) whose nonlinearity in many cases exceeds the current best known values. Moreover, we design some balanced functions (for odd $n$ ) that also achieve the highest nonlinearity known.