Oh. The root note. The world may never know… 
I entered the ToybOx chord (D C# F) into this site: http://www.gootar.com/piano/
It offers three possible names. Each is a four note chord missing one note:
C# -9 no5
D m maj7 no5
F aug5 6th no3
So the root can be any of the three notes depending on which chord you think it is.
The search for the lost chord continues…
The root note is whatever note you start with first
ie D F C# -> root = D
F C# D -> root = F
C# D F -> root = C#
Secretly we all know its 42.
Or is it? 
i like triads which involve a interval with 11 semitones of difference (in your case that would be d3 and c#4) but it doesn’t work so well with all types of timbres… some instruments are much more forgiving and it sounds smoother.
using the same notes (really the same pitch classes… d can be d0, d1, d2, etc. so just saying d doesn’t mean one knows exactly which pitch we are talking of) but just one semitone apart (d3 and c#3) is harder to get to sound smooth but you can get a cool “beat interference” type of effect. http://en.wikipedia…eat_(acoustics)
also, since you like the set of pitch classes (the set of notes) d, c#, f why not, unless you already have, try out all the inversions of them? (then you’ll have tried all the notes as root notes)
if you wanna try the inversions:
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play d3, f3, c#4
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move the highest note down one octave and you’ll get c#3, d3, f3 (probably the most dissonant of the three… can’t check now though).
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repeating the step above again: move f3 down one octave and you get the third set of pitches f2, c#3, f3.
Cmon guys!! He said he is writing in D Harmonic minor!! So if he wants to fit the chord in a way thats makes sense with his song the root note will be D!! 1st inversion of course(not that ppl should know that bit, actually about bass note as opposed to root) 
how u actually want to strcucture the chord, of course depends on how it sounds, Maes’ advice is right on 4 this 
I think that ToybOxes note progression is unfinished, because chord progression suggested by Progressor tool ends up with dissonant chord. Two notes added to this progression lead to consonance:
If you do not know what chords go underneath a scale, then how can you be writing in ‘D Harmonic Minor’? 
(and that’s not slant on toyb0x)
CDEFGABC is a scale (C Major) over a C Major progression, for example C F G (I IV V)
Same notes, starting with F:
FGABCDEF is still C Major if played over the same chords (C F G) but if played with a tonal centre of F (over a correct progression), it becomes F Lydian. For example, F G Em (I II v)
It could be G Mixolydian, or B Locrian or…it depends on context ie what chords are underneath
Picking D C# and F out of the air does not make nor imply any scale (and in the truest sense, if you’re implying a scale (in this case D Harmonic minor), it should be D F C#)
It’s got nothing to do with inversions or bass notes
At the end of the day, the OP asked what the root note was, if he’s feeling D, then D it is. Everything else might be ‘out of tune’ but his tune, his chords, his choice
There not picked out of the air,there from the scale im working in,i know its d harmonic minor because the rest of the chord progression is made up of the usual set of chords from the set of notes that make the scale up.make sense?
Well, the chord is dm maj7 with no fifth. The fifth isn’t really relevant tonally, at least when all the notes you have are D C# and F. Here D is the root, F is the third and C# is the major 7th. If you wanna find out how you harmonize scales, just google it, and you will learn about stacking thirds. It’s really quite easy. But i have to say that even though dmmaj7 is the correct root chord of the d harmonic minor scale, it’s not really used that much because of it’s unpleasing sound. Most often you play a straight d minor and use some other instrument to create the melody and bring out the major 7th which is the dissonant part of the scale. I think 
Thank you kind sir,you have answered all my woes!