If I understand you right you want to re-construct your signal with the same tone frequencies and amplitudes but force the phase of each tone to, for example, zero (independantly of its actual phase).
If you are in LabVIEW you can for example use the Extract Single Tone Information high-level VI to detect the exact frequency and amplitude of each tone and then re-construct the waveform in the time domain using the detected freq. and ampl. and the phase of your choice.
Hint: If you want to extract the information for multiple tones, use the VI in a loop and export the residual signal after each run to be used as input signal for the following run.